The carbon footprint of the cold chain logistics system refers to the greenhouse gas emissions directly or indirectly caused in each link of the cold chain logistics activities. Because cold chain logistics is the main carbon emitter in the field of logistics, research on how to reduce carbon emissions in the field of cold chain logistics plays an important role in energy conservation and emission reduction. Based on the in-depth analysis of the carbon footprint of cold chain logistics, this paper introduces the distance coefficient and freshness parameters into the optimization model innovatively and uses the life cycle assessment method and input-output method to determine the calculation range of the carbon footprint of fresh products of each link in the cold chain logistics. The system calculates the carbon emissions generated by the production and operation activities of each place of origin, distribution center, retailer, and waste disposal during the circulation of fresh products. This paper establishes a carbon footprint optimization model to discuss how to balance carbon constraints and minimized costs. Through the analysis of the simulation results, from the perspective of the government and enterprises, corresponding countermeasures are put forward to more effectively achieve the goal of energy conservation and emission reduction and guide the cold chain logistics industry to sustainable development.