The green production behaviors of farmers in protected areas (PAs) can reduce environmental disturbances and contribute to the effectiveness of PAs. Based on a survey of 708 farmers in Wuyishan National Park (WNP) and Crested Ibis Nature Reserve (CINR), we studied the influence of perceived benefit and policy incentive on farmers’ organic fertilizer application. Results: (1) Perceived benefit, subsidies policy, and propaganda policy significantly promoted farmers’ organic fertilizer application, with perceived benefit having the strongest effect, followed by subsidies policy. The influence of restriction policy was not significant. (2) Perceived benefit, subsidies policy, and propaganda policy indirectly influenced organic fertilizer application through ecological awareness. (3) In WNP, perceived benefit had the strongest effect on organic fertilizer application, and subsidies policy significantly enhanced farmers’ ecological awareness and influenced their behaviors. In contrast, subsidies policy had the strongest effect on organic fertilizer application, but did not significantly enhance farmers’ ecological awareness in CINR. These results offer valuable insights for promoting green production behaviors of farmers in PAs. This study implies that there must be a pathway for the realization of ecological value in ecological protection. Ecological value realization is the endogenous motivation for farmers’ sustainable green production behaviors. However, government subsidies and guidance are also essential in the early stage.