Restoration of submerged macrophytes is one of the important measures for ecological treatment of eutrophic lakes. The changes in physical and chemical conditions caused by submerged macrophytes also affect the process of benthic nitrogen cycling. The growth period of Potamogeton crispus is mainly in winter. In order to understand the effect of submerged macrophytes growing in winter on nitrification rate and denitrification rate in the process of nitrogen cycling, experiments were carried out from winter to summer with vegetated and non-vegetated treatments. The results showed that the effect of submerged macrophytes on water temperature was not significant in winter. The nitrogen cycling was mainly affected by variables, which were inorganic nitrogen and dissolved oxygen. Submerged macrophytes had little effect on nitrification rate, but had a certain inhibition on denitrification rate by providing oxygen from photosynthesis. In total, submerged macrophytes growing in winter have little effect on nitrogen cycling in sediment. However, submerged macrophytes growing in winter can increase the attachment surface of microbes and inhibit resuspension of sediment, which play a complementary role to submerged macrophytes growing in summer for maintaining stability of eutrophic lakes.