Promoting quality certification of agricultural products is a matter of the sustainable development of agriculture and the transformation of the global agri-food system, and cooperatives are an important carrier to achieve the above policy goals. However, few scholars have included external resources and cooperative quality certification behavior in an analytical framework from the perspective of resource embedding. This study combines resource dependence theory and embeddedness theory, based on survey data from 230 agricultural cooperatives in six counties of Sichuan Province, China. This paper constructs a theoretical analysis framework of government resources, market resources and cooperative quality certification, and uses binary Logit regression model to empirically study the correlation between external resources and cooperative quality certification. The results show that: (1) Cooperatives do not receive a high proportion of external resource support, with 30% and 47% receiving support from the government and market respectively; the proportion of cooperatives carrying out product quality certification was relatively low, about 29.57%. (2) Government resources and market resources have a significant positive effect on improving the quality certification of cooperatives, and the promotion effect of the market is greater than that of the government. (3) Mechanism analysis shows that government resources promote quality certification in cooperatives mainly through regulations on agricultural inputs, while market resources can jointly play a role on regulations on agricultural inputs and market expectations for certified agricultural products.