Based on the data of Yunnan, Guizhou, Sichuan and Chongqing from 2009 to 2021, the systematic GMM method was used to empirically analyze the effect of tax incentives on regional innovation efficiency. The empirical results show that tax incentives can significantly improve the innovation efficiency of Yunnan, Guizhou, Sichuan and Chongqing. In economically developed areas, the innovation incentive effect of tax incentives is more obvious, while in economically underdeveloped areas, tax incentives have no significant impact on regional innovation efficiency. Based on the conclusions drawn from the empirical analysis, the corresponding policy suggestions are put forward to improve the preferential tax policies and formulate differentiated preferential tax policies.