In light of the growing emphasis on “logistics integration,” this paper contends that the logistics network system requires comprehensive integration and optimization. We propose the use of the Bacterial Foraging Optimization (BFO) algorithm to enhance the Vehicle Routing Problem (VRP). The penalty function method is employed to direct the BFO algorithm in identifying the optimal vehicle path encoding and to improve the convergence operations for logistics distribution. This study analyzes the fundamental characteristic elements of the VRP, introduces a basic model for the VRP, and develops a logistics distribution path optimization model that minimizes the total cost by thoroughly considering the expenses associated with cold chain low-carbon logistics distribution. A simulation environment is established, and algorithm parameters are set to determine the optimal solutions for both the BFO and the Improved BFO (IBFO) algorithms in the test function. An example is selected for practical application, wherein the design of the distribution center and points is carried out, and the colony intelligence optimization algorithm is applied to simulate the logistics and distribution paths. Combined with the specific case of cold chain distribution of food, the optimization of the cold chain logistics distribution path is solved. In the case study, when the carbon penalty coefficient is ε = 15, the optimal logistics and distribution site selection program is Guangxi and Guizhou, and the total cost of the supply chain is 16,363,365.92 yuan. At this time, the supply chain cost is optimal. Compared with the carbon penalty coefficient ε = 20, the economic cost increased by 70152.24 yuan, but the carbon emission decreased by 1890.9 kg. The optimization of logistics and distribution processes encourages enterprises to develop strategies that promote low carbon and environmental protection and achieve better economic and ecological outcomes.