Plant variety rights are essential for agricultural development and food security. This paper mainly starts with the cost-benefit issue of plant variety rights that enterprises are concerned about, and introduces the cost-benefit analysis method into the research and development, application, and protection of plant variety rights. This research takes the new plant variety rights as the research object, clarifies the development status of the world plant variety rights from the perspective of time series development characteristics and spatial distribution pattern, explores the location of the variety rights in the world, and uses methods such as knowledge measurement and data mining, to carry out in-depth research on the application and authorization of plant variety rights, the scope of protection catalogues, the structure of variety rights, and the applicant unit. Finally, the regression model is tested from five aspects: regression model significance test, model goodness-of-fit test, Hosmer goodness-of-fit test, goodness-of-fit test, and overall accuracy test of model prediction. The regression coefficient of plant variety rights cooperation in the research process was 1.908, and the statistical test value was significant at the 5% level ( P = 0.022 < 0.05 ). Using system dynamics to evaluate its risks, it provides new ideas for the risk analysis and prevention of seed industry enterprises’ variety rights capitalization operation.