Due to the continuous trade friction between China and the United States, for domestic enterprises in China, the cost of importing foreign technologies is increasing. Thus, the independent research and development (R&D) becomes particularly important for the realization of green technology innovation (GTI). This paper establishes a non-linear mediating effect model based on the data of various regions in China from 2012 to 2018. The main results are shown in the following. Firstly, there is an inverted U-shaped relationship between the intensity of intellectual property protection (IPP) and the level of GTI. Furthermore, the independent R&D investment has a masking effect between them. Secondly, by taking the independent R&D investment as a threshold variable, we prove our findings. Considering that the intensity of IPP is at a high level in most regions of China, the above statements mean that the enterprises need to continuously increase their investment in R&D, in order to further improve the regional ability in GTI. Meanwhile, local governments should also stimulate enterprises' willingness to expand their scale in R&D by issuing incentive policies, such as R&D tax incentives and government subsidies.