To further improve the coordination of government innovation policy operation and the efficiency of implementation, and dig out the optimal innovation “combination boxing” strategy that can effectively stimulate enterprise innovation behavior, it is urgent to deeply explore and evaluate the actual effects of different innovation policy tools and their combinations. When evaluating the effectiveness of innovation policies, especially the multi-tool combination, both self-selection of enterprises for policies and government agencies’ picking-the-winner strategies often lead to endogenous issues. The multi-level treatment effect model is used which can effectively identify the multi-tool combination, and the actual effect of different innovation policy tools and their policy-mix on the innovation behavior of enterprises in China is evaluated, under the premise of effectively solving the endogenous and selection bias issues. To satisfy the random distribution conditions of causal inference, the multi-level treatment effect model should meet the Conditional Independence Assumption (CIA) and the Overlap Assumption (OA), and the functional expression of conditional expectation value of enterprise innovation can be written as . Thereby, the Average Treatment Effect (ATE) when the treatment level changes from to can be estimated. Based on the data of listed enterprises in China from 2009 to 2019, it is found that the multi-tool combination consisting of direct subsidy, tax incentive and government procurement tools may become the government’s optimal implementation strategy of innovation policy, both in stimulating the R&D input and the innovation quality of enterprises. From the perspective of stimulating substantive innovation, government multi-tool combination is more suitable for state-owned enterprises. From the perspective of stimulating strategic innovation, the optimal strategy does not exist. It not only helps to evaluate the effect of innovation policy combination scientifically and reasonably, but also provides empirical basis and practical guidance for improving the design of innovation policy system in this study.