Here, we compared the effects of marine DHA-enriched phosphatidylcholine (DHA-PC) and EPA-enriched phosphatidylcholine (EPA-PC) on high bone turnover in a model of osteoporosis induced by bilateral ovariectomy in vivo, and further investigated the possible protective mechanisms. Meanwhile, DHA-PC and EPA-PC clearly ameliorated the microstructure of the trabecular bone and accelerated bone mineral apposition rate, additionally increasing bone mineral density and biomechanical properties of the bone. Furthermore, gene and protein expression levels suggest that DHA-PC and EPA-PC inhibited overactive osteogenesis via down-regulation of the expression of the osteogenesis-related Wnt/β-catenin signaling pathway. In conclusion, DHA-PC and EPA-PC reduced excessive osteogenesis via normalization of Wnt/β-catenin expression. These results may contribute to the elucidation of the anti-osteoporotic properties of DHA-PC and EPA-PC and further develop their potential application value as a functional food.