Abstract: Considering carbon emission, time windows, cargo loss and other factors, with the goal of minimizing distribution costs, this paper constructs an optimization model of the cold chain logistics distribution path of fresh agricultural products by calculating cost of carbon emission through carbon tax. Combined with the examples, the genetic algorithm is used to gain the solution, and the cold chain logistics path optimization scheme of fresh agricultural products is calculated with and without considering carbon emission respectively. The comparative analysis results show that considering carbon emission factors can effectively control and improve circulation rate of fresh agricultural products and reduce loss rate of fresh agricultural products. Logistic distribution costs are controlled and carbon emission is reduced, which provides effective decision-making for fresh supermarkets to optimize cold chain logistics and distribution.