In order to study the relationship between sediment ecological desilting depth and pollutant content, the sediment in the Lake area of Huizhou was taken as the research object, the pollution risk of total nitrogen, total phosphorus and heavy metals in sediment and the effect of nitrogen and phosphorus adsorption-desorption equilibrium concentration on the dredging depth were studied. The results showed that the potential ecological harm index of heavy metals in the sediment of the lake area was at the low risk level. The comprehensive pollution index of TN and TP was in the heavy pollution level, with an average of 3.55 and 8.55, respectively. The average adsorption and apportionment equilibrium concentrations of NH3-N and P in pollution layer, transition layer and normal lake mud layer are 1.41 mg/L, 1.14 mg/L and 0.86 mg/L, which have a great risk of pollution release. It was suggested that the pollution layer and transition layer should be dredged with an average dredging thickness of 54.41 cm.