This study used high-throughput sequencing technology to analyze the community structures, assembly processes, and functional differences of abundant and rare bacterial sub-communities in the farmland topsoils with different distances below the prevailing wind direction of a phosphorus chemical industrial area. The results showed that Actinobacteria, Proteobacteria and Chloroflexi were the dominant bacterial phyla in both sub-communities. The diversities of two sub-communities in soil sample close to industrial area with high Cd content were lower than those in the other distant soils with low Cd contents. Significant differences in community compositions were observed between these two soil types, while their functional compositions were similar. Correlation analysis showed that soil pH and Cd were the main factors affecting the two bacterial sub-communities, with the former being more critical. Rare bacteria maintained higher community and functional diversity compared to abundant bacteria. Neutral modeling analyses indicated that community assembly processes of abundant and rare bacterial sub-communities were represented by stochastic and deterministic processes, respectively.