Aim to study that different enhanced oil recovery processes influence microbial community in the oil reservoir, three different types of samples from Ng3 zone of Shengli oilfield were analyzed: produced water from water-flooded well, from heterogeneous combination flooding well and from microbial enhanced oil recovery process. Based on 454 pyrosequencing of 16S rRNA gene amplicons, microbes clustered into Proteobacteria were dominantly detected in the three samples. However, Dominant microorganisms in three production wells were significantly different at genus level. The majority of reads obtained in three samples were aligned closely to Azospirillum, Pseudomonas, and Thauera, respectively. The microorganisms usually detected in oil reservoirs environments and associated with members of Azospirillum, Pseudomonas, Thauera, Acinetobacter and Petrobacter. Microbial communities in production well after nutrients injection, revealed an activation of the microbes, and some microorganisms were significantly inhibited with a sharp decline in the number. This first investigation of the microbial diversity in oil reservoir with different enhanced oil recovery processes expands substantially the knowledge of the extent of microbial diversity and highlights the complexity of microbial communities.