As an important means of agricultural production, seeds are of great significance in ensuring grain security. The development of the seed industry in China started relatively late, and there is a “bottleneck” problem of seed provenance in some fields. From the perspective of the distribution of plant variety rights, this paper analyzed the problems of seed provenance “bottleneck” problem faced by China through international comparison by using the application and authorization data of variety rights of China and the International Union for the Protection of New Varieties of Plants (UPOV) members from 2010 to 2020, and identified a corresponding solution path. Results show that the breeding technology was developing continuously in China, and the number of residents’ applications for variety rights increased rapidly. However, the authorization rate declined. Compared with UPOV members, the main applicants for variety rights in China were mainly from domestic applicants. Currently, China is facing the following major “bottleneck” problems of seed provenance: relatively lag behind biological breeding technology, insufficient protection of germplasm resource mining and utilization, low protection level of plant variety rights, and imbalanced structure of plant variety rights, especially for the seeds of vegetables, flowers and herbs, which mainly depend on import. Therefore, this paper provides the following suggestions: breaking through the “bottleneck” technology research, strengthening the introduction, development and utilization of crop germplasm resources, improving the protection system and protection level of new plant varieties, constructing the commercial breeding system of deep cooperation among government, industry, university, and research institutes, and strengthening the early warning of seed security risks.