The gamification design of Citizen Science Projects has not yet formed a unified and systematic theoretical research results. Researchers lack a quantitative evaluation index system to guide and evaluate the gamification design of citizen science projects. After combing the literature related to the evaluation index of gamification design, the study constructs the evaluation index system of gamification design of citizen science projects. This evaluation index system includes four dimensions: educational goals, scientific goals, game interaction experience, and system security. After collecting the data of experts and analyzing the weight coefficients of each index by using the analytic hierarchy process (AHP), this study finds that education and science are still the main considerations of citizen science projects' gamification design, while users' game interaction experience and system security are in the secondary position, which suggests that researchers are more likely to use gamification as an auxiliary design tool. Finally, the evaluation index system is used to evaluate the gamification design of the Foldit project. The shortcomings of the gamification design in the existing public science projects are summarized, and the future gamification development strategies are put forward.