The microbial enhanced oil recovery (MEOR) method is an eco-friendly and economical alternative technology. The technology involves a variety of uncertainties, and its success depends on controlling microbial growth and metabolism. Though a few numerical studies have been carried out to reduce the uncertainties, no attempt has been made to consider temperature, pressure, and salinity in an integrated manner. In this study, a new modeling method incorporating these environmental impacts was proposed, and MEOR analysis was performed. As a result, accurate modeling was possible to prevent overestimating the performance of MEOR. In addition, oil recovery was maximized through sensitivity analysis and optimization based on an integrative model. Finally, applying MEOR to an actual reservoir model showed a 7% increase in oil recovery compared to waterflooding. This result proved the practical applicability of the method.