Revealing soil microbial community stability of different long-term fertilization strategies is helpful to guide field fertilization management and ensure soil health and sustainable development of agroecosystems. Based on the long-term stationary field experiment on nutrient balance in the Fengqiu National Agro-ecological Experimental Station of the Chinese Academy of Sciences, the experiments of drought disturbance and rewet recovery were carried out on three different fertilization strategies of Fluvo-aquic soils. The microbial community stability (resistance and recovery) was quantified and compared in terms of dehydrogenase activity, bacterial alpha diversity, key taxa, community structure and molecular ecological network. The results showed that compared with no fertilization (CK) and mineral NPK fertilizers (NPK), organic manure plus mineral NPK fertilizers (OM) significantly increased the resistance and recovery of the microbial community. After rewet treatment, soil alpha diversity recovered faster than community function and structure. Soil alpha diversity, the abundance of key taxa and network topology parameters recovered to the initial level, while dehydrogenase activity and community structure did not recover completely. This study quantified and compared the microbial community stability of three different fertilization strategies from a variety of microbial community response indexes. The results showed that the application of organic manure plus mineral NPK fertilizers could significantly improve the stability of the microbial community, which is a good fertilization management strategy to ensure the soil health and sustainable development of the farmland ecosystem.