[Objective] To investigate the effects of fertilization regime alterations on microbial communities in paddy soils. [Methods] We conducted a long-term field experiment with three treatments: chemical fertilizer (H) and H converted to a conventional amount of organic fertilizer (HC), a conventional amount of organic fertilizer (C) and C converted to chemical fertilizer (CH), and a high amount of organic fertilizer (G) and G converted to chemical fertilizer (GH). Metagenomic sequencing was combined with bioinformatics analysis to assess the structures, diversity, and co-occurrence networks of microbial communities in paddy soils. [Results] Compared with the H treatment, the HC treatment increased the soil organic carbon, dissolved organic carbon, total nitrogen, and alkali-hydrolyzable nitrogen (P<0.05). The CH and GH treatments exhibited lower soil carbon and nitrogen levels than C and G treatments, respectively. The HC treatment markedly altered the relative abundance of Acidobacteriota, Nitrospirota, Candidatus Rokubacteria, Mucoromycota, and Thaumarchaeota. The CH treatment showed no significant changes in microbial composition at the phylum level, whereas the GH treatment significantly modified the relative abundance of Nitrospirota and the archaeal community structure. Although fertilization regime alterations showed no significant effect on microbial alpha diversity (P>0.05), the beta diversity differed across treatments (P<0.05). Co-occurrence network analysis demonstrated that the HC treatment enhanced the network complexity relative to the H treatment, with increased nodes (181), edges (2 935), average degree (16.215), modularity (0.757), and clustering coefficient (0.495). The CH treatment showed more edges (3 894) and higher average degree (21.514) but lower modularity (0.599) than the C treatment (0.751). Conversely, the GH treatment diminished all network topology parameters relative to G. Redundancy analysis identified dissolved organic carbon (22.1%), soil pH (16.8%), total nitrogen (15.6%), ammonium nitrogen (14.6%), available potassium (11.8%), and available phosphorus (10.6%) as the primary drivers of microbial community variations. [Conclusion] The findings indicate that fertilization regime alterations influence the microbial community structure and network characteristics in paddy soils by modifying soil physicochemical properties. Transitioning from chemical to organic fertilization enhances microbial community stability and soil ecological functions, while replacing organic with chemical fertilization reduces soil carbon and nitrogen availability, potentially compromising microbial network complexity and resilience.