Abstract: Fossil energy bioengineering is an emerging interdisciplinary field that integrates geology, microbiology and energy engineering. Its core lies in utilizing microbial-driven mechanisms to achieve clean conversion of fossil energy, regulation of greenhouse gas emissions and synergetic enhancement of CCUS. With the Earth’s critical zone as the core, the lithosphere (carrier of fossil energy), biosphere (carrier of microorganisms), atmosphere, and hydrosphere are integrated to construct a “Four Spheres and Three Zones” theoretical model. This framework systematically elucidates the spatiotemporal differentiation patterns of microbial-driven organic matter metabolism. In the shallow oxidation zone and weak reduction zone, organic matter degradation is predominantly mediated by aerobic bacteria, with the concomitant release of greenhouse gases including CO₂ and N₂O. In the deep reducing zone, anaerobic methanogens are the dominant functional group, which efficiently convert organic matter or CO₂ into methane and facilitate its accumulation and reservoir formation. Further proposed is the theoretical concept of the “Fossil Energy Microbial Carbon Pump” (FEMCP), which elucidates that the lithosphere functions as a critical carbon carrier while microorganisms act as the core engine. Through three interconnected subsystems—input (carbon sources), transformation (biocatalysis), and output (products)—this pump drives the directional cycling of carbon across the four spheres. A research method for fossil energy bioengineering has been established: in the shallow surface field, long-term in-situ fixed-point monitoring and gradient-coupled microcosm experiments are combined to evaluate the greenhouse gas emission potential of organic rocks. In surface conversion, an integrated technology for microbial catalytic conversion of coal is developed, focusing on the biological liquefaction pathway of low-rank coal. Components of coal liquefaction products are systematically analyzed, and the application potential of coal-based carbon quantum dots as photosensitive materials is explored. In the field of deep coal reservoirs, in-situ temperature-pressure coupled bacterial enrichment and cultivation technology is established, multi-pathway strategies for enhancing microbial functions such as biology, physics, and chemistry are developed, and a specific implementation process for coalbed methane bioengineering is proposed. This discipline focuses on three core application directions. The mechanism of microbial degradation of shallow organic matter-bearing rocks and the resulting greenhouse gas generation and emission patterns is revealed. Taking the Jurassic carbonaceous mudstone in Yima, Henan and the Upper Triassic oil shale in Jiyuan as examples, field fixed-point monitoring found that greenhouse gases are released all year round, indicating that the release of greenhouse gases from shallow organic rocks under the action of microorganisms is long-term and periodic, further verifying the greenhouse gas emission potential of the microbial carbon pump and confirming that H₂ is a non-greenhouse gas with a greenhouse effect. Regarding the microbial catalytic conversion of coal, laboratory simulations have confirmed that the microbial liquefaction rate of low-rank coal can reach 59.14%. In addition to a variety of chemical products, high-value carbon quantum dots were found in the coal liquefaction products. Using them as photosensitizers to provide photoelectrons can promote heterotrophic microorganisms to fix CO₂ and produce 600 mg/L of acetic acid. For deep reservoirs, a bioengineering technology has been developed to efficiently convert coal, residual coal in goafs, residual oil in depleted oil and gas reservoirs, and injected CO₂ into methane or high-value chemical products under in situ conditions. Physical simulations have demonstrated that under in situ reservoir conditions, coal and shale can produce 7.8 and 3.1 mL/g of biomethane, respectively, while residual coal in goafs yields 2.3 mL/g of methane. Meanwhile, the goafs are filled with coal-based solid waste at a density of 450 kg/m³, and CO₂ is sequestered at a rate of 100 kg/t of solid waste. Coke oven gas injected into coal reservoirs can be effectively converted into CH₄ through microbial catalysis, achieving an H₂, CO₂ conversion rate of over 95%. Under the reservoir conditions of 55 ℃, the efficiency of CO₂ microbial methanation increased by 68.3% compared to 35 ℃, with a cumulative conversion volume of 8.50 m³/t. In a depleted oil reservoir, the co-injection of CO₂ and bacterial solution yielded methane production of 11.8 mL/g from residual oil. At the same time, the potential for CO₂ storage through microbial methanogenesis under reservoir conditions and its multi-path synergistic sequestration through dissolution, mineralization, and adsorption is being explored in depth. This discipline, through underground and surface bio-factories, is driving the transformation of fossil energy from fuel to feedstock, providing core technical pathways for green energy development, resource utilization of industrial coal-based waste, and carbon neutrality.