The fruit crop industry plays an important role in agricultural production and rural development in China. Germplasm is the basis both for the industry and for breeding. In the context of seed industry revitalization, it is of great significance to systematically assess the current progress in fruit crop germplasm and look forward to its future development, thus to help realize the goal of self-reliance and self-control of seed sources in the seed industry. This study summarizes the significant progress made in fruit crop germplasm research in China from the aspects of collection, preservation, evaluation, and utilization, analyzes the main problems, and looks forward to future development directions. A great progress has been achieved, but compared with developed countries, there still exists a considerable gap in the areas of collection, innovative utilization, information database construction, germplasm sharing, and virus-free germplasm preservation. In this regard, it is recommended to strengthen the collection of fruit crop germplasm both domestically and internationally; prioritize systematic efforts in precise germplasm identification, discovery of superior genes, and germplasm innovation; build a national information platform for germplasm; improve the mechanism of germplasm sharing; accelerate the development of virus-free germplasm resource centers; and prioritize their preservation and sharing. These measures will better support the high-quality development of China’s fruit crop industry.