The deepening impact of the “Belt and Road” on the opening-up and trade development of the countries along the route has put forward higher requirements for cross-border logistics and transportation of e-commerce enterprises. In this paper, enterprise A is selected as an example object of analysis, and the Improved Adaptive Genetic Algorithm (IAGA) is used to optimize the cross-border e-commerce logistics network, realize the rational planning of the cross-border e-commerce logistics network, reduce the cost of cross-border e-commerce logistics enterprise logistics and transportation, improve the efficiency of resource utilization, and enhance the timeliness of logistics and transportation. The study shows that IAIGA can solve the problem of lack of dynamic adaptability existing in IGA, with faster convergence speed, better convergence stability, higher optimization accuracy, and can provide technical support for solving parameter identification problems. Meanwhile, the constructed optimization model and the designed improved genetic algorithm IAIGA to solve the cross-border e-commerce logistics network optimization problem are feasible and effective, and the relative error rate of IAIGA algorithm is no more than 1.8%, which can reduce the logistics and transportation cost of enterprises by 1%~8%.