Variety innovation is the key to seed industry revitalization. It is necessary to identify judicial decision-making factors of statutory damages in variety right infringement cases, in order to enhance the level of judicial protection for variety rights, thereby stimulating breeding innovation. Using cases of statutory damages for infringement of variety right from 2002 to 2023 samples, this study analyzes their spatiotemporal characteristics analysis, establishes a multiple regression model, to explore reference factors and influence factors of statutory damages amount. The results show that the application of statutory damages for variety rights infringement is generalized and the awarded amount is relatively low. Legislative measures to raise upper limits of statutory damages have minimal effects. The reference factors of statutory damages lacks quantitative standard, and the position of reasonable litigation expenses is unclear. Factors such as anchoring effect and judicial experience have significant influence on judicial decision-making. To improve the quality and effectiveness of judicial protection of variety rights, the following measures are recommended: overcoming the generalization of statutory damages by strict application of statutory damages to eliminate evidentiary barriers and lower proof standard; avoiding subjectivity in the judgment by establishing standards and rules for calculating compensation amounts and separating calculation of reasonable expenses; reducing anchoring effect and ensuring fairness in judgments by improving the quality of judicial decision-making information, enhancing the professionalism of judges, and providing judicial decision-making space.