The red lines for ecological protection is an important policy tool to protect regional ecological functions, ensure national ecological security, and promote sustainable development. However, there are many problems, such as the short-term conflicts between ecological protection and economic development, an overlapping of ecological space and living space of farmers in the red line area, and an interlacing of ecological fragility and poverty, pose challenges to the implementation of the red lines for ecological protection policy. This paper takes Youyang and Chengkou, whose ecological protection red line area is large in Chongqing, as an example, to analyze the impact of the current red lines for ecological protection policy on farmers' livelihoods and the effect that the ecological compensation have on this conflict. The results are: first, the current red lines for ecological protection policy has indeed affected economic development and farmers' livelihoods, making farmers feel that their interests have been "deprived" and their sense of access to ecological rights is reduced; second, market-oriented and diversified ecological compensation mechanism is an important means to effectively improve the livelihood status of farmers in the red line area, and corresponding government governance suggestions are put forward.