This paper addresses the problems existing in the current two-way logistics and distribution model of rural e-commerce and proposes the study of rural e-commerce distribution efficiency with the technical support of intelligent logistics. Based on the knowledge of multi-objective optimization theory, the maximization of distribution efficiency of logistics enterprises and the maximization of demand coverage as the objective function, while the constraints are vehicle load, service time, path constraints, and finally, complete the construction of the multi-objective optimization model of rural e-commerce logistics and distribution efficiency. According to the NSGA-II algorithm with low computational complexity, fast operation speed, and good convergence, the NSGA-II algorithm is used to solve the constructed model, and then the optimal solution of rural e-commerce logistics distribution efficiency is derived. With regional logistics as the research subject, a multi-objective optimization model for rural e-commerce logistics distribution efficiency supported by intelligent logistics technology is simulated and analyzed. The data show that compared with other algorithms, the NSGAII algorithm has a smoother learning curve oscillation, while the final result of convergence (-1.473), the objective function is smaller (20.42), and the optimal total transportation time is smaller (609.22s). Finally, in order to solve the current rural e-commerce logistics and distribution problems in part, from the improvement of rural e-commerce logistics and distribution system, strengthen the rural logistics infrastructure construction of the two aspects of rural e-commerce logistics and distribution efficiency improvement strategy.