In this study, soil samples were collected from seven different long-term treatments in the maize-wheat rotation area of northern Anhui. The 16S rRNA gene amplicon sequencing using Illumina technology was used to investigate the effects of organic fertilizer substitutions for partial chemical fertilizers on soil bacterial sub-community characteristics and physicochemical properties. The results showed that long-term application of chemical fertilizers significantly reduced soil pH, while the use of organic fertilizer could mitigate soil acidification. In addition, the long-term application of organic fertilizers and straw returning significantly increased the contents of soil organic matter and available nutrients. In terms of bacterial sub-communities, the substitution of organic fertilizer for partial chemical fertilizers did not significantly alter their diversities but significantly changed their compositions. Proteobacteria, Acidobacteriota, and Chloroflexi constituted the dominant phyla under all treatments. Proteobacteria significantly increased while Acidobacteriota significantly decreased in abundance when organic fertilizer partially replaced chemical fertilizers. Analysis of Levins' niche breadth index revealed that the ecological niche breadth of abundant taxa was considerably higher than that of rare taxa. The results of Mantel tests and RDA showed that pH significantly influenced both abundant and rare bacterial sub-communities, with rare taxa demonstrating a greater sensitivity to environmental factors.