This study used high-throughput sequencing technology to analyze the community structure, assembly process, and functional differences of abundant and rare bacterial sub-communities in the farmland surface soil 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 diversity of two sub-communities in soil samples close to industrial area with high Cadmium (Cd) content was lower than that in the other distant soils with low Cd content. Significant difference in community compositions was observed between these two types of soil, 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.