In this article, the actuality of internal and overseas study of Microbial Enhanced Oil Recovery numerical reservoir simulation was analyzed for the sake of further studying of the process of MEOR. At the same time, the author brought forward a series of effective threedimension and threephase mathematical simulation models and solved them by use of finite implicit difference method, and then discussed the approach to gain the parameters. These equations were tested by use of a typical geological model. At the same time, the microbial waterflooding were contrasted and normal waterflooding, then the influence factors (microbe and nutrition concentration, slug structure, interlayer permeability, etc.) and parameter optimization of MEOR were discussed.