[Objective] To study the properties of endogenous microorganisms in Weibei Oilfield, we studied the ability of biosurfactant production, crude oil degradation and enhanced oil recovery on core displacement model of the isolated hydrocarbon oxidizing bacteria. Furthermore, we evaluated the effects of huff and puff field trial to discuss the process and feasibility for microbial enhanced oil recovery in ultra-low permeability and shallow reservoir. [Methods] We collected oil-water samples from ultra-low reservoirs and isolated surfactant producing hydrocarbon oxidizing bacteria by crude oil plate, identified the isolates by the physiological-biochemical properties and 16S rRNA gene sequence analysis, and then determined their environmental adaptation. Furthermore, we used an endogenous and exogenous microbial compound system to evaluate the abilities of crude oil degradation and enhanced oil recovery on both sand-pack and core-flooding physical model. Finally, the highly optimized microbial system was performed by the huff and puff process in a production well. [Results] A hydrocarbon oxidizing bacterium Pseudomonas aeruginosa, named WB-001, was isolated from ultra-low permeability reservoir in Weibei Oilfield. The fermentation broth surface tension and wax concentration were reduced to 29.04 mN/m and 8.48%, respectively. Sand-packing model and core displacement experiments showed that the oil displacement efficiency was 9.72% and 12.54%, respectively, performed with WB-001 and OPUS-HOB-001 compounding fermentation liquor injection compared with water flooding. The field trial showed that the daily oil production was increased from 0.42 t to 0.89 t, and total oil increase production was 44.47 t after microbial huff and puff process. In addition, the laboratory experiments on collecting samples showed that oil viscosity, freezing point and fluid surface tension was reduced by 11.70%, 9.41% and 18.93%, respectively. [Conclusion] This successful field trial proved that microbial enhanced oil recovery has its applicability in ultra-low permeability reservoirs and provides theoretical reference and a novel approach to high oil production of tight and ultra-low permeability reservoirs.