This paper seeks to effectively realize energy saving and emission reduction in the process of location for fresh agricultural cold chain logistics. It is based on the traditional location for distribution center optimized for both freshness and carbon emissions. A bi-objective function location model was constructed to minimize the total cost and carbon emission and a two-stage heuristic algorithm was designed to solve the model. According to analyzing the location case of Y enterprise in Zhejiang Province, the THA had an average total cost optimization rate of 7.70% and an average carbon emission optimization rate of 10.23% compared to the WOA, while it had a rate of 12.77% and 14.12%, respectively, compared to the PSO. When the unit carbon emission cost increased from 0.02 dollar/kg to 0.06 dollar/kg, the comprehensive carbon emission cost increased by 42.07% and the total cost increased by 3.05%. Therefore, logistics enterprises can achieve the reduction of logistics costs and sustainable development through reasonable location for fresh agricultural products cold chain distribution centers.