Lake eutrophication remains a serious environmental problem of global significance, and phosphorus (P) plays a key role in lake eutrophication. Internal P loading, as a result of P release from sediments, is gathering more and more recognition as an important source governing the P availability in these ecosystems. Anoxic condition can promote the release of P associated with Fe oxides, which has already been a consensus. However, it is still unknown whether the anoxic conditions induced by eutrophication act to intensify or weaken the regeneration of organic P (P_org) in sediments. We selected the Hongfeng Reservoir, a typical sub-deep lake, to study the regeneration behaviours of C and P in the sediments buried before and after eutrophication. The results showed that P_org did not significantly increase with the rapid increase in organic C (C_org) since eutrophication occurred. Furthermore, the organic C/P ratio was much higher in sediments buried after eutrophication than in those buried before, which indicated that P_org regeneration had been significantly enhanced since eutrophication occurred. Based on C/P ratios, our estimation suggested that the P_org regeneration and P release from sediment to water approximately enhanced 45.2% ± 8.7% and 34.5% ± 9.8%, respectively. Elevated primary productivity (algae) and the corresponding hypoxic/anoxic condition, both caused by eutrophication, promoted P biogeochemical cycle in the sub-deep reservoir. This study further verifies the significant contribution of regenerated P_org to the internal P load, and highlights the importance of controlling P release from sediments in order to restore clear water ecosystems in sub-deep lakes or reservoirs.