To study the utilization and budgets of nitrogen and phosphorus in higher-place aquaculture ponds of gentian grouper （Epinephelus lanceolatus ♂ × Epinephelus luscoguttatus ♀），and to illuminate the dynamics of water quality and the sources and fate of nitrogen and phosphorus，during 55 days of cultivation，fish，pond water，input and output water and feed were regularly sampled and analyzed in three higher-place ponds. The results showed that： （1） the average concentration of dissolved oxygen during culture was between 8.64 and 9.55 mg/L； Ammonia nitrogen，nitrite，nitrate and phosphate showed irregular fluctuation in the three ponds； The contents of total nitrogen and total phosphorus varied from 6.14 to 7.11 mg/L and 0.38 to 1.41 mg/L，indicating serious eutrophication of the aquaculture pond. （2） During the cultivation period，the survival rate of gentian grouper was high. The weight gain rate of fish and feed conversion ranged from 96.0% to 227.0% and 0.55 to 0.90. The utilization rates of feed nitrogen and phosphorus were 47.0%-59.0% and 52.0%-63.0%，respectively. （3） Feed accounted for 61.0%-66.8% of total nitrogen input and 66.9%-71.0% of total phosphorus input. Fish harvest from the ponds accounted for 43.0%-60.9% of nitrogen output and 45.0%-67.7% of phosphorus output. The rest of the nitrogen and phosphorus were exported as drainage，sediment and other ways. The results of the study showed that higher-place aquaculture ponds of gentian grouper had high level nitrogen and phosphorus content， feed is the major way of nitrogen and phosphorus input to the pond and fish harvest is the major way of nitrogen and phosphorus output. The rest output was discharged through aquaculture effluents. Appropriate management of the waste water discharge in aquaculture is needed to decrease negative effect on nearby waterbody.