Green product certification (GPC) is an important means of eliminating the asymmetry of information between consumers and manufacturers in the context of sustainable development. This study examined the critical risk factors in GPC and provided relevant suggestions for managers to reduce risk and ensure the correctness of the process. First, 18 risk factors were summarized along four dimensions: the certification institution, the entrusting enterprise, the certification business, and the implementation of the certification. Second, the Delphi method was used to determine the formal research framework, and the decision-making trial and evaluation laboratory (DEMATEL) method was applied to analyze the causal relationships among the risk factors to identify the ones driving risk and those representing the outcomes of GPC. This was used to construct a causality diagram of the risks related to green certification. Finally, the analytic network process (ANP) method was used to calculate the weight of each risk factor, and the weighted prominence of each is calculated to identify the critical factors. The results showed that the working life and experience of the certification institution were the critical driving risk factors in GPC. Corresponding countermeasures were also proposed to mitigate these risk factors.