Soil microbe and soil enzyme activities are closely related to the fertilizer inputs. Our objective was to explore the dynamic change of soil microbe and soil enzyme activities in paddy field during early and late rice (Oryza sativa L.) main growth stages with different long-term fertilizer managements in the double cropping rice system. we analyzed the soil microbe and soil enzyme activities with mineral fertilizer alone (MF), rice residues and mineral fertilizer (RF), 30% organic matter and 70% mineral fertilizer (LOM), 60% organic matter and 40% mineral fertilizer (HOM), and without fertilizer (CK) basis on long-term fertilizer experiment. The results showed that the soil enzyme activities were increased by application of mineral fertilizer along with manure or rice residues at the main growth stages of early and late rice. The soil urease activities for different fertilizer managements was RF>HOM>LOM>MF>CK at the main growth stages of early and late rice. The soil catalase activities with HOM, LOM treatments was highest, and was significantly higher than that of RF, MF, CK treatments at the main growth stages of rice. The soil invertase and dehydrogenase activities with HOM treatment were highest, and were significantly higher than that of CK at the main growth stages of rice. And the soil cellobiohyrolase activities with RF treatment were highest, and were significantly higher than that of MF, CK treatments at the main growth stages of rice. Meanwhile, the results indicated that different fertilization managements were significantly affected some physiological function soil microbial quantity. The amount of nitrifying and denitrification bacteria in soil for different fertilizer managements was HOM>LOM>RF>MF>CK at the main growth stages of early and late rice. Meanwhile, the amount of ammonifiers and cellulose”decomposing bacteria in soil for different fertilizer managements was MF>RF>LOM>HOM>CK and LOM>RF>MF>HOM>CK at the main growth stages of rice, respectively. The amount of azotobacteria in soil with RF treatment was highest, and was significantly higher than that of MF, CK treatments at the main growth stages of rice. As a result, the soil microbe and soil enzyme activities were increased by applied of fertilizer practices, the effect of mineral fertilizer combined with manure or rice residues is better than that of only mineral fertilizer.