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Science and technology innovation (STI) policy is a strategic principle to guide the whole cause of STI. The study on STI policy and its effect is particularly important. Most of the existing studies on the effect of STI policy focus on the effect of a single policy, and the studies on the effect of policy combination and its differences need to be further enriched and improved. This study proposes a method combining system simulation experiment and analysis of variance (ANOVA) to study the differences of combination effects of STI policies. The results show that there are significant effect differences in the combination of STI policies as a whole, but when it comes to different combinations of STI policies, not all policy combinations have significant differences. This study not only points out whether there are significant differences in a certain effect among which combinations of STI policies but also points out whether there are significant differences in all effects among which combinations of STI policies at the same time. This study has theoretical and practical significance for realizing scientific policy-making and sustainable development. [ABSTRACT FROM AUTHOR]