As an important component of aquatic germplasm resources, freshwater aquatic germplasm resources play a crucial role in building an all-encompassing approach to food, ensuring food security, and guaranteeing the effective supply of high-quality proteins. Socio-economic development and intensified human activities pose threats to freshwater aquatic germplasm resources, and the conservation, utilization, and security of these resources have attracted widespread attention. This study reviews the current status of China’s freshwater aquatic germplasm resources from the perspectives of natural and cultured germplasm resources, and clarifies the conservation situation of these resources from three aspects: conservation system, conservation measures, and conservation effectiveness. The study indicates that China's conservation system of these resources needs optimization, the preservation and evaluation technology system is yet incomplete, biodiversity conservation is insufficiently emphasized, and the legal framework needs improvement. Furthermore, the following measures are proposed: (1) strengthening the preservation, identification, and exploration of aquatic germplasm resources; (2) accelerating technological innovation and application in freshwater aquaculture; (3) enhancing diversified conservation measures for aquatic germplasm resources; and (4) improving the legal system for the conservation of aquatic germplasm resources. These measures can effectively improve the conservation and utilization of freshwater aquatic germplasm resources and promote the high-quality development of aquaculture.