Aquatic products have become the third most important source of food protein after cereals and milk all over the world. Fifteen percent of food protein intake for a global population of 7 billion people originates from aquatic products. In China, the largest production and consumption country in the word, aquatic products meet 30% of animal protein demand for its people. It is a global scientific goal to maintain the sustainable and stable supply of aquatic products, where aquaculture genetic breeding plays an important role. Aquaculture breeding is a research hot spot in which countries all over the world compete for development. The development of breeding technology and the cultivation of fine varieties fully reflect comprehensive innovation strength and market competitiveness of the country. Since the 1950s, artificial spawning, insemination and hatching of silver carp (Hypophthalmichthys molitrix) and bighead (Aristichthys nobilis) were realized, which marked China taking the leading role in the technology and theory of artificial propagation of freshwater fish in the world. After that, China's aquaculture breeding has achieved great achievements in scientific research and made irreplaceable contribution to the development of the industry. Carrying out genetic breeding research on aquaculture species can improve the intensity of germplasm resources development and the depth of gene resources mining, exploit the scientific and technological potential of China’s aquaculture seed industry, and enhance the level of industrial application. Aquatic breeding in China covers two major systems, namely, the breeding and promotion of new varieties, which has become the top priority to promote the green development of the aquaculture industry. It has demonstrated outstanding effectiveness in ensuring stable and high-quality protein supply, enhancing competitiveness of China as a seed industry powerhouse as well as improving people's eating and consumption habits. With the rapid development of life science, especially molecular biology and genomics, China’s aquaculture breeding has achieved fruitful scientific research results, but also encountered many bottlenecks and constraints. This paper synthetically summarizes the significance of carrying out aquaculture breeding research and analyzes the general situation of aquaculture breeding research in China. We also present the key problems that need to be tackled and solved, whose focus was mainly on four aspects. Firstly, the efficiency of germplasm resources utilization was still lower. Secondly, the traits owned by the cultivated varieties were not diverse enough. There are, in addition, seldom new techniques applied in the process of breeding and the imperfect commercial breeding system. On the basis of the research goals, the key scientific and technical tasks in the future are proposed that involve strengthening the excavation and efficient utilization of germplasm resources, attaching importance to fundamental research to strengthen source innovation, developing cutting-edge technologies to tackle key problems as well as focusing on market demand to cultivate excellent new varieties. Relevant countermeasures and suggestions are also made, such as building a germplasm resources conservation system, constructing a platform to support innovation, promoting the policy support for protection, and creating new research and development entities, etc. In summary, it is expected the information of this review could provide reference materials for China to lead the world in aquaculture breeding research and the transformation and upgrading of fisheries in the new era.