The germplasm resources of freshwater fish are relatively abundant in China, and the quantity of their species is enormous, which account for a vital part in the high-quality protein supply from aquatic animals. However, the growth, development and reproduction of freshwater fish are seriously affected by frequent occurrence of fish diseases and culture environment stress, which restricts the healthy sustainable development of freshwater aquaculture industry. In order to solve these two main challenges, it is an effective way to carry out further research on genetic improvement and breeding of resistant traits and cultivate new freshwater fish varieties with better resistance abilities. This article comprehensively reviews the basic status of breeding improved varieties of freshwater fish with disease resistance and anti-stress, summarizes the review of new varieties of freshwater fish with disease resistance or anti-stress traits from 1996 to 2023, and introduces the resistant performance indicators, adopted technical routes and actual breeding effectiveness of representative breeding new varieties. Focusing on five types of traits, namely disease resistance, cold resistance, hypoxia tolerance, low temperature tolerance, and saline-alkali tolerance, this article reviews the main research progress in accurate evaluation of genetic parameters, excavation of trait linkage markers, and analysis of molecular regulatory mechanism. Combined with the current research status of disease resistance and anti-stress of major freshwater aquaculture fish in China and advanced typical cases at home and abroad, this article summarizes the outstanding problems in current breeding research, such as the slow progress of cultivating new varieties with excellent resistance performance, the lag in research and development of high-throughput measurement technology for phenotypic traits, the insufficient depth of analysis of hereditary basis and regulatory mechanism of traits, and the weakness of breeding and industrial application of varieties that take into account multiple traits. With focuses on the outstanding problems faced by the breeding of resistant traits in cultured freshwater fish at present, this paper proposed to carry out research tasks in four aspects, the high-efficiency conservation and utilization of germplasm resources in cultured freshwater fish, the analysis of genetic mechanism and molecular regulatory of disease resistance and anti-stress traits, the cultivation of new varieties and germplasm creation with excellent resistance abilities, and the parental maintenance and popularization of new resistant varieties. In summary, it is expected the information of this review could provide references for researches on breeding of resistant traits of major cultured freshwater fish in China.