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Microbial phosphate removal from wastewater sewage is a promising and feasible technique that increases the ability of a sewage treatment system to remove phosphate from wastewater. Maintaining a healthy population of phosphate-solubilizing bacteria is the key premise of biological sewage treatment. Chitosan is used to remove dissolved phosphorus from the water column during wastewater treatment. The present study found that chitosan has another function in phosphorus removal, affecting the diversity and community composition of phosphate-solubilizing bacteria. We obtained 16S rRNA genetic data by using a shotgun metagenomic sequencing method. Data indicated that phosphate-solubilizing Pseudomonadaceae was the dominant bacteria population, after adding chitosan to the dynamic water treatment process. In chitosan-enhanced treatments, populations were 35.11% larger than the control group. Chitosan addition also caused some increases in the population sizes of Rhodocyclaceae, Bacillaceae, and Enterobacteriaceae, but the addition of chitosan had little effect on Hyphomicrobiaceae and Sphingomonadaceae in the activated sludge. Moreover, the Chao1 estimator, the abundance-based coverage estimator (ACE), and Shannon index all indicated a very high diversity of bacteria when chitosan was added. Finally, we determined that chitosan increased the activity of the enzymes phytase, dehydrogenase, and phosphatase, which enhance the degradation rate of phosphorus in the activated sludge of a D-A2O system. We suggest that chitosan plays an important role in dissolving organophosphorus during sewage treatment.