To successfully simulate the anaerobic metabolic process of Indigenous Microbial Enhanced Oil Recovery (IMEOR) and reduce the risk of practice test, a new mathematical model was established for porous flow field-microbial field coupling in anaerobic metabolic process according to the study on anaerobic microbe chain composed of fermentative bacteria, nitrate reducing bacteria, sulfate reducing bacteria and methanogen, and the solution of this model was given. The effect of IMEOR in anaerobic metabolic process relies on the regulation of microbe community. Equations about porous flow field affected by microbe in the model not only elaborate the impacts of microbe and three primary metabolic products (bio-surfactant, bio-polymer, bio-gas) on physical parameters, but also reflect the main mechanisms (emulsification, profile modification and viscosity reduction) for microbial enhanced oil recovery. Equations in microbial field influenced by fluid flow could indicate the substance distribution decided by fluid flow and the collaborative metabolism relationship on biological chain formed by microbe community. The coupling of porous flow field and microbial field should be solved together. The model supplies theoretical basis for the study on IMEOR mathematical model software.