The key to improve the effect of water flooding development of low permeability reservoir is to solve the problem of multi-scale water channeling in low permeability oil fields. An endogenous microbial plugging agent was developed and the formula of the fermentation nutrient solution for the plugging agent has been optimized. Subsequently，the basic physical properties of the plugging agent were characterized through indoor static experiments and the plugging adaptabilities of the plugging agent were evaluated through dynamic core experiments. The fermentation nutrient solution of the strain was consisted of 1.0%—2.0%molasses，0.2% —1.0% sodium nitrate，0.5% —2.0% potassium dihydrogen phosphate，0.2% —1.0% disodium hydrogen phosphate，0.1%—0.5% ammonium sulfate，0.01%—0.1% industrial yeast extract，0.01%—0.03% ferric sulfate and 0.01%—0.03% manganese sulfate. After cultivation in the fermentation nutrient solution for 4 days，the growth of microbial strains stabilized. The formed dispersed particles exhibited a normal distribution with particle sizes of 40—160 μm and a median granularity of about 90 μm. The prepared microbial plugging agent had good shear resistance，salt resistance and stability. The initial state of microbial plugging agent could be injected into the low-permeability core，heterogeneous core and fractured core with good injectivity. The microbial strains could grow and reproduce in the cores based on the characteristics of self-growth，and match with the spatial scale of pore media or fracture media，which could not only plug the porous medium with different scales， but also plug the micro-fractures with different scales. The plugging rate of the core with a permeability of 5×10^-3 μm² reached up to 80%. As for the heterogeneous parallel composite cores with the permeability of 5×10^-3/100×10^-3 μm² and 5×10-3/300×10^-3 μm²，the plugging rate reached up to 92% and 95%，respectively. For the fractured cores with an opening of 30 μm and 80 μm，the plugging rate reached up to 84% and 90%，respectively. The microbial plugging agents could plug both porous medium with the different scales and micro fractures with the different scales based on the characteristics of self-growth，thus possessing the potential to plug the multi-scale water channeling in low-permeability oil reservoir.