Microorganisms play an important role in soil ecosystems, especially in commercial rice paddy fields. However, it is not understood how organic fertilizers affect microbial communities in these fields. In this study, we used different long-term fertilization treatments (i.e., no fertilizer, chemical fertilization, and 25% - 100% organic fertilizer) to investigate their effects on soil fungal and archaeal communities, rice yield, and soil physicochemical properties, and the interactions of these indicators. The results showed that the organic replacement treatments had a significant effect on the assembly of soil microbial communities in rice fields, while different microbial taxa showed different response patterns to the organic replacement treatments. Species composition and community assembly process of fungal community were more sensitive to the response of organic replacement treatment, and alpha diversity of archaeal community was more sensitive to the response of organic replacement treatment. OM, HN, Phosphatase, and TP were the common soil indicators significantly associated with the three microbial groups, among which OM was the most influential indicator in this study. A total of 18 biomarkers were obtained by difference analysis, distributed in Ascomycota, Basidiomycota and Chytridiomycota. In addition, we obtained the keystones in the community through network analysis and found that the organic replacement treatments affected the microbial keystones by altering the soil HN and OM content, which in turn led to the alteration of the soil microbial community. This study provides new insights into the effects of different fertilization regimes on soil bacterial, fungal and archaeal communities, and also provides a theoretical basis for rational and balanced fertilization in agricultural production.