With the popularity of Internet technology, the changing needs of consumers and the transformation and upgrading of the retail industry, new retail has emerged. The industrial structure shows a trend towards green, and people begin to pursue the quality and safety of products, and also green consumption, putting forward higher requirements for the supply chain. A green supply chain performance evaluation index system for fresh e-commerce enterprises containing six indexes is constructed, which includes: procurement costs, storage costs, packaging costs, transportation costs, distribution costs and information costs. Then, based on the realistic requirements of the green supply chain performance evaluation model for fresh e-commerce enterprises, a fuzzy comprehensive evaluation system model is established which uses the deviation maximization weighting method to determine the evaluation index weights and uses the intuitionistic hesitancy fuzzy method and Vlsekriterijumska Optimizacija I Kompromisno Resenje (VIKOR) method for comprehensive evaluation. Finally, an empirical analysis is conducted with Freshippo as an example to verify the applicability and objectivity of the performance evaluation index system and the evaluation model. The results show that Freshippo is at the upstream position of the industry and the new retail industry has more room for improvement.