To compare the budget of nitrogen and phosphorus in Megalobrama amblycephala, which was cultivated in separated pond and sequencing pond,two kinds of ponds were selected for sample analysis, from August to November 2016, with the traditional pond as the control. The results showed that feed was the main source of nitrogen and phosphorus of Megalobrama amblycephala in ponds. The feed input proportion of nitrogen was traditional pond(68.53%) < separated pond(72.03%) < sequencing pond(76.22%). The feed input proportion of phosphorus was traditional ponds (42.87%) < separated pond (53.37%) < sequencing pond(56.64%). In these three kinds of ponds, the most important expenditure of nitrogen was sedimentation and water discharge. Among them, sedimentation and water discharge of nitrogen in the sequencing pond was the lowest, followed by the separated pond, and the traditional pond was the largest. The most important expenditure of phosphorus was aquaculture outputs. As for the proportion of phosphorus in aquaculture output to total phosphorus output, the highest is separated pond, up to 54.55%, the traditional pond is 52.20% and the sequencing pond is 43.38%. The results showed that the proportion of nitrogen and phosphorus sedimentation and water discharge in separated pond and sequencing pond was lower than that of traditional pond. It can reduce the nitrogen and phosphorus sedimentation and water discharge, increase the utilization rate of nitrogen and phosphorus, and improve the efficiency of feed utilization by constructing separated pond and sequencing pond. In particular, sequencing pond was used to raise the efficiency of material utilization in Megalobrama amblycephala farming.