Sediments in the water level fluctuation zone of the reservoir undergo frequent drying and flooding processes due to water level changes. In order to investigate the effect of drying process on nitrogen and phosphorus in the sediments, the study analyzed sediment samples collected at different elevations in the water level fluctuation zone of the Biliuhe Reservoir. Subsequently, a drying simulation experiment was carried out based on the field survey to explore the characteristics of nitrogen and phosphorus morphology change in the sediments of the water level fluctuation zone during the drying period, so as to provide a reference for the management of endogenous pollution in reservoirs. The results showed that TN content reduced by 2.99% under the influence of denitrification; however, as the conditions under which denitrification occurred were destroyed by water evaporation, the TN content gradually stabilized. Affected by mineralization, there was a morphological transformation of organic phosphorus (OP) to inorganic phosphorus (IP), which improved the bioavailability of phosphorus. Moreover, an enrichment of nitrogen and phosphorus to the surface layer was seen during the drying period. Therefore, sustained drying condition is conducive to the removal of excess nitrogen from the sediments, which in turn contributes to plant growth and primary productivity in the water level fluctuation zone.