Promoting the development of eco-industries plays a significant role in achieving the harmonious symbiosis between economic growth and environmental protection as well as enhancing the comprehensive effectiveness of ecological and economic benefits. Due to their unique nature, cooperatives may play a crucial role in facilitating the integration between farmers and the development of eco-industries. To investigate whether cooperatives possess the capacity to enhance the income-generating effects for farmers involved in eco-industries, this study selected the Crested Ibis National Nature Reserve (CINNR), a representative area for eco-industry development, as the research site. Data were gathered through face-to-face interviews, and this research empirically analyzed the impact of cooperatives on the income-generating effect of farmers using endogenous switching regression (ESR). The findings are threefold. First, cooperatives indeed enhance the income-generating effects for farmers engaged in eco-industries. Second, variables such as the distribution of agroforestry materials, premium capacity, soil quality, and status of village cadres have a positive impact on farmers joining cooperatives, whereas punishment initiatives discourage their participation. Third, for farmers who have joined cooperatives, factors such as the distribution of agroforestry materials, premium capacity, low-cost conservation initiatives, land area, status of village cadres, the proportion of labor force, technical training, soil quality, and land area positively affect their income from eco-industries. Conversely, punishment initiatives, age, and land location negatively impact their income. The results of this study provide new ideas for farmers to participate in the development of eco-industries, new evidence showing co-operatives can improve farmers’ income, and new directions for coordinating conflicts between conservation and development in protected areas.