In order to explore the treatment capacity of an integrated wastewater treatment system for freshwater pond aquaculture wastewater, this study selected an aquaculture base with an integrated wastewater treatment system in Chongqing. According to the water quality evaluation indexes in "Requirement for Water Discharge from Freshwater Pond Aquaculture " (SC/T 9101-2007), the water quality of aquaculture wastewater and effluent from various treatment units was measured and analyzed. The results showed that the annual average suspended matter content (TSS), 5-day biochemical oxygen demand (BOD5), permanganate index (CODMn), total nitrogen (TN), and total phosphorus (TP) removal efficiencies were 67.30%, 77.13%, 39.31%, 48.39% and 52.62% in the comprehensive wastewater treatment system, and the removal effect was obvious. After the wastewater treatment system is used to treat the aquaculture wastewater, the treated aquaculture wastewater is all lower than the level 1 standard of "Requirement for Water Discharge from Freshwater Pond Aquaculture ", and the wastewater can be directly discharged or recycled. The research shows that the integrated wastewater treatment system has an obvious effect on the treatment of aquaculture wastewater, and can effectively control the pollution index of aquaculture wastewater, which has a positive significance for improving the aquaculture environment and reducing aquaculture pollution.