The effects of fertilization on soil microbial diversity and ecological functions have been widely studied, but whether diversity and functions respond in similar ways remains unclear. Bacillus is a keystone taxon for improving soil productivity in agricultural systems. In this study, samples were collected from five long-term fertilization experimental sites. Bacillus communities were enriched using heat selection, and amplicon sequencing coupled with metagenomic sequencing was integrated to characterize their responses to fertilization. Our results showed that the response of Bacillus diversity to fertilization exhibited a clear spatial pattern, primarily driven by background soil physicochemical properties. Balanced fertilization, such as the combination of chemical and organic fertilizers, directionally shaped the metabolic traits of Bacillus, enriching functional genes involved in carbon metabolism and nutrient transformation. In contrast, under no fertilization, the community was dominated by endogenous carbon metabolism and energy metabolism. Additionally, phosphorus metabolism-related functional genes were positively correlated with Bacillus richness and evenness, whereas nitrogen metabolism functions showed a negative correlation with evenness, revealing a link between soil microbial diversity and metabolic functions. Taken together, our study reveals the differential responses of Bacillus diversity and metabolic functions to fertilization, offering new perspectives for optimizing fertilization management.