Based on natural resource-based theory, this study constructed a relational model between green intellectual capital, green innovation, and an agricultural corporate sustainable competitive advantage. The samples included a total of 341 agricultural companies in China, and multiple regression methods are used for the analysis. The results showed that green product innovation and green process innovation had a mediation effect between green human capital, green structural capital, green relational capital, and the sustainable competitive advantage of agricultural corporate. Beyond the simple moderation effect, a new integrated moderated-mediation effect model was established. It was shown that environmental leadership, green organizational identification, and green dynamic capability had different moderated-mediation effects under different conditions. The study is expected to close the previous research gaps and insufficiency in agricultural corporate environmental management and green agricultural. The empirical results and conclusions bring enlightenment and meaningful theoretical guidance to managers, researchers, practitioners, and policy makers in the green and sustainable development of agricultural corporates. The new environmental management path can help agricultural corporates conduct green innovation effectively, adapt to the green agricultural products market, and achieve sustainable competitive advantage. Ultimately, this will help to accelerate the development of green agriculture.