By constructing a Stackelberg game model in two competing supply chains, this study investigates how the government subsidy policies (no subsidy, unit cost subsidy, and green technology investment subsidy) and consumer preference affect a new energy vehicles (NEVs) manufacturer’s eco-innovation level, profit, and social welfare. The results show that under a given subsidy policy, as the proportion of NEVs-oriented consumers increases or the proportion of oil-fueled vehicles consumers decreases, the NEVs manufacturer’s eco-innovation level increases. Furthermore, compared to the scenario without subsidy, the government subsidies increase the NEVs manufacturer’s eco-innovation level and profit. In the case of subsidies, when the proportion of NEVs consumers is high, the government should provide the unit cost subsidy, otherwise, it should provide the green technology investment subsidy.