Microbial Enhanced Oil Recovery (MEOR) is an option for recovering oil from depleted reservoirs. Numerous field trials of MEOR have confirmed distinct microbial community structure in diverse production wells within the same block. The variance in the reservoir microbial communities, however, remains ambiguously documented. In this study, an 8 m long core microbial flooding simulation device was built on a laboratory scale to study the dynamic changes of the indigenous microbial community structure in the Qizhong Block, Xinjiang oil field. During the MEOR, there was an approximate 34% upswing in oil extraction. Based on the 16S rRNA gene high-throughput sequencing, our results indicated that nutrition was one of the factors affecting the microbial communities in oil reservoirs. After the introduction of nutrients, hydrocarbon oxidizing bacteria became active, followed by the sequential activation of facultative anaerobes and anaerobic fermenting bacteria. This was consistent with the hypothesized succession of a microbial ecological “food chain” in the reservoir, which preliminarily supported the two-step activation theory for reservoir microbes transitioning from aerobic to anaerobic states. Furthermore, metagenomic results indicated that reservoir microorganisms had potential functions of hydrocarbon degradation, gas production and surfactant production. Understanding reservoir microbial communities and improving oil recovery are both aided by this work.