The reform of environmental management systems is key to improving environmental pollution treatment and green technology innovation. Based on panel data on 30 provincial administrative regions in China for 2008 to 2016, this paper analyzes the impacts of environmental decentralization and environmental protection investment on green technology innovation. It is first found that environmental decentralization promotes green technology innovation after inhibition. Similar effects are found for environmental administrative decentralization, environmental monitoring decentralization, and environmental supervision decentralization. Second, in the long run, environmental decentralization in developed and low-emission regions is more conducive to green technology innovation. Third, environmental pollution treatment investment has a significant inhibiting effect on green technology innovation under high levels of environmental decentralization, and the inhibiting effects of industrial pollution source treatment investment and “three simultaneous” construction project investments are particularly obvious. This paper explores green technology innovation as the goal of environmental decentralization, which is the driving force behind pollution control. From the perspective of environmental protection investment, the paper further analyzes the impact of environmental decentralization on green technology innovation. The study has important reference value for determining reasonable levels of environmental decentralization among different levels of governance and in formulating differentiated strategies of environmental decentralization.