Revealing soil microbial responses is helpful to guide field management practices, which is promising to promote the sustainability of farmland ecosystems. But the indicator species at the regional scale are unclear. In this study, six paddy experiment sites spanning across subtropical China were used to investigate the effects of long-term application of chemical fertilizer and chemical fertilizer plus organic fertilizer on soil microbial community. The inconsistent of microbial species caused by soil geographical distribution were firstly denoted. After that, paddy soil microbial community shifted in a consistent manner with nutrient addition. Long-term fertilization increased soil total nitrogen, available phosphorus and organic matter contents, which changed soil microbial community, mainly increasing relative abundance of Chloroflexi, Proteobacteria, Acidobacteria, Nitrospira and Chlorobi. Compared with chemical fertilizer, chemical fertilizer plus organic fertilizer application further increased the species that are associated with macromolecular organic matter conversion and that mostly belong to copiotrophic bacterial taxa, such as β-Proteobacteria, Anaerobes, Ignavibacteria, Bacteroidetes and Firmicutes.