Fertilization is one of the most common agricultural practices to achieve high yield. Although microbes play a critical role in nutrient cycling and organic matter decomposition, knowledge of the long-term responses of the soil bacterial community to organic and inorganic fertilizers is still limited. This study was conducted to evaluate the effects of century-long organic (manure), inorganic (NPK), and no fertilization (control) treatments on soil bacterial community structure under continuous winter wheat (Triticum aestivum L.) cultivation. Fertilization treatments altered the richness, diversity and composition of the soil bacterial community. Compared with the control, manure significantly increased the operational taxonomic units (OTUs), Chao 1 and Shannon indices, and taxonomic groups, while NPK significantly decreased these parameters. Fertilization treatments did not alter the types of dominant phyla but did significantly affect their relative abundances. Acidobacteria and Proteobacteria were the most dominant phyla in all treatments. Manure led to enrichment of most phyla, with a diazotrophic group, Cyanobacteria, being an exception; NPK reduced most phyla, but enriched Chloroflexi; control led to promotion of Cyanobacteria. Soil pH and NO3− were two dominant parameters influencing the bacterial community structure. Soil pH positively correlated with the relative abundances of Proteobacteria and Gemmatimonadetes but negatively correlated with those of Acidobacteria and Chloroflexi; NO3− negatively correlated with the relative abundance of Cyanobacteria, which was 14–52 times higher in control than the fertilized soils. Cyanobacteria, especially M. paludosus and L. appalachiana, could be the key players in maintaining wheat productivity in the century-long unfertilized control.