Although diazotrophs are major participants in biological nitrogen fixation (BNF) processes, the variations in community structure and assembly processes in response to long-term fertilization with different fertilizer application are still ambiguous, especially under various doses with balance or not. Using nifH amplicon sequencing, we investigated the soil diazotrophic communities in a paddy field which received 20-year fertilization including control (CK), balanced fertilization (three doses of nitrogen (N), phosphorus (P), and potassium (K) at same ratio (NPK, 2(NPK), and 3(NPK)), unbalanced fertilization (three ratios, (2 N)PK, N(2P)K, and NP(2K)), and manure (M). Our results showed that the diazotrophic diversity increased with the long-term fertilization, but it was tapering-off with doses increment. However, the community dissimilarities increased with fertilizer doses. These variations were attributed to the trade-off between the variation of soil pH and nutrients. The increasing of fertilizer doses induced the transformation of community assembly processes, which changed from mainly dominated by deterministic processes in CK, NPK, NP(2K) and M to stochastic processes in the other treatments. Our findings suggest that the long-term fertilization, especially different fertilizer doses, strongly affect soil diazotrophic diversity, community structure, and assembly processes, which could help to improve the sustainable agricultural management in the future.