With the continuous expansion of rural logistics, it has become increasingly important to build a logistics system with emergency resilience. In order to solve the problems of insufficient emergency service capacity in the last kilometer of rural logistics, backward information technology, and insufficient resource integration, this paper designs a county and village three-level logistics collaborative distribution model based on the background of digital economy. The evaluation index system is built through literature research, and the simulation model of rural logistics collaborative distribution system is constructed by using system dynamics method. Finally, taking Beijing rural area as an example, the system model is studied for benefit assessment and the accuracy of the simulation model is verified.