Green supply chain management is a crucial way to balance economic benefits and environmental impacts. As an important economic aquatic product in China, sea cucumber (Apostichopus japonicus) is facing the dual challenges of economic benefits (profit) and environmental sustainability (material input and emission output). Currently, the sea cucumber industry in China lacks a green supplier screening system, resulting in a fragmented pattern of cooperation among enterprises. Core enterprises in the supply chain cannot assume social responsibility to help and guide upstream and downstream enterprises to jointly improve environmental performance. This study focuses on the selection and evaluation of green suppliers for sea cucumber processing enterprises. Firstly, a green supplier assessment indicator system for sea cucumber processing enterprises was established, and the indicator weights were determined by the analytic hierarchy process (AHP) method. Next taking a large sea cucumber processing enterprise in Dalian, China, as an example, the importance level of each index was evaluated by fuzzy comprehensive evaluation (FCE), and the score and ranking of existing suppliers were determined. The validity and practicality of the method were verified. The results show that Supplier 1 (S1) has the highest score, and the price of sea cucumber farming, the cleaner production level of sea cucumber farming, environmental awareness, and long-term cooperation willingness were the most important factors in the selection of green suppliers for sea cucumber processing enterprises, which provides useful clues on the best practice of making sustainable development decisions. With an in-depth understanding of the key factors, suppliers can formulate different prices according to the differences in sales channels to improve the economic deficiencies. Environmental pollution can also be reduced by using clean energy, establishing a recirculating aquaculture system, and using micro-ecological preparations. The conclusions of this study can provide technical support and decision-making suggestions for the application of green supply chain management in China’s aquaculture industry.