Polyculture is an effective way to achieve efficient utilization of nutrient resources in high-density intensive aquaculture systems. In order to study the optimal culture mode of Oreochromis niloticu, Aristichthys nobilis, and Cherax quadricarinatus, the budget of nitrogen and phosphorus in various polyculture systems (CH, CHC1, CHC2, CHC3) was studied with land-based enclosures. The results showed that all the three polyculture systems had higher total yields of cultured animals than the control group (two polyculture systems) (p < 0.05). The co-cultured organisms absorbed artificial feed or organic matter (such as plankton and sediment) from the polyculture system to different degrees. Feed was the main input of nitrogen (98.22–98.33%) and phosphorus (99.43–99.56%) in all systems. Considering the N and P outputs, 46.64–64.58% and 81.60–84.79%, respectively, accumulated in the sediment, and 34.43–52.55% and 14.89–17.30% of the N and P outputs, respectively, were harvested by aquaculture organisms. The pollution production coefficients of TN and TP in the O. niloticus polyculture ponds were 5.35–6.26 g/m2 and 1.17–1.61 g/m2, respectively. The TN production coefficients of O. niloticus and the ternary polyculture groups (CHC1, CHC2, and CHC3) were lower than that of the control group (CH). The TP production coefficients showed the opposite pattern. The N and P utilization efficiencies in the group with the optimal ratio of O. niloticus, A. nobilis, and C. quadricarinatus (4, 0.15, and 3 ind/m2, respectively) were 2.56–12.82% and 6.62–11.03% higher, respectively, compared with those of the other groups. The N utilization efficiency was effectively improved in this group with the optimum stocking density for the polyculture systems, resulting in improved ecological efficiency and economic benefits.