[Background] The indigenous microbial community in the porous medium of the reservoir is the basis for the indigenous microorganism enhanced oil recovery. Because of the difficulty and high cost of the sampling technique from porous media in the reservoir, the spatial distribution of indigenous microbes from the injected into the output of porous media after the indigenous microorganism flooding has not been clarified. [Objective] simulation of indigenous microbial enhanced oil recovery process was done via long core dynamic continuous displacement experiment. The spatial distribution of the indigenous microbial communities from injection to output end was revealed by analysis the internal microbial community structure adsorbed on the oil sand of different spatial loci after implementation. [Methods] The microbial community structure adsorbed on the oil sand of different space sites of core was analyzed by the high-throughput sequencing and fluorescent quantitative PCR. [Results] from injection to output end, the difference in the ecological environment of porous media and microbiological interaction lead to the spatial difference of the microbial community. There has been a clear law of aerobic to anaerobic succession. Aerobic microbes are mainly distributed in the front of the core, such as Pseudomonas, which can drive the crude oil in the front of the core by producing the biological surfactants. Facultative and anaerobic microorganisms such as Geobacillus and Anaerobaculum are mainly in the middle of the core, while anaerobic bacteria and methanogens are mainly at the end of core. Anaerobic bacteria produce H2, CO2 and small molecular acids through the anaerobic metabolism of organic nutrition, which provides a metabolic substrate for the methanogens at the end of the core. [Conclusion] aerobic and anaerobic succession spatial distribution of indigenous microorganisms in the porous media was clarified for the first time, and the understanding of the indigenous microorganisms in the reservoir was further deepened.