The adjustment of China's new energy vehicle (NEV) industry policies and innovation incentives is currently in progress. This study takes a new perspective by comparing subsidized and non-subsidized policies, and empirically examines their innovation effects on NEV enterprises using the innovation value chain theory. The results indicate that in the previous technology development stage, the subsidized policy exhibits a relatively stronger but volatile impact on incremental innovation, whereas the non-subsidized policy demonstrates a more stable effect on radical innovation. In the latter innovation value realization stage, both policies show a better impact on the short-term innovation value (output value) of NEV enterprises compared to the long-term value (market value). The mediation effect and threshold effect tests show that there is a significant mediating effect of technology development behavior of NEV enterprises in the whole value chain, although the specific mediating pathways and threshold effects are inconsistent, and overall innovation transmission efficiency is insufficient. Moreover, considering the internal ownership of NEV enterprises and external regional innovation atmosphere characteristics, the effects of the two policies also have their own distinct emphases. This study provides new insights for addressing issues related to innovation incentives and policy decisions for NEVs in the post-subsidy era.