Aiming at the problem of how to use the remaining oil of Class I conglomerate reservoir in the’ double high’ stage, the field test of 4-injection and 11-production endogenous microbial flooding was carried out in the Keshang Formation reservoir of Q District, Kelamayi Oilfield, Xinjiang from 2013 to 2022. The field effect shows that the variation characteristics of oil increment, concentration of functional bacteria and biochemical indexes of oil wells in the test area show obvious regional regularity. The functional genes of type I wells in the south are significantly higher than those of type II wells in the middle and type III wells in the north. In order to clarify the influencing factors that affect the effect of microbial oil displacement, this paper starts with the formation development model and analyzes the internal configuration of the reservoir in the test area based on the fine sedimentary research. It is clear that the thickness of the source formation in the test area gradually decreases, the vertical source formation is equal to the thickness development, and the microbial test well group has a good correspondence between injection and production wells. The complexity and serious heterogeneity of the permeability distribution in the test area are studied. The remaining oil in each small layer is controlled by the sedimentary configuration interface and is distributed in a strip shape. It is divided into remaining oil between wells, remaining oil affected by the configuration interface, and remaining oil in isolated sand bodies. The remaining reserves abundance of type I wells in the main layers is mostly high, and the structure is relatively low. The geological conditions of the reservoir are the main factors affecting the effectiveness of the oil wells in the microbial test area, which provides a basis for guiding the adjustment of the microbial flooding field test plan and effectively evaluating the microbial flooding effect.