<p>This paper focuses on the design and optimization of the logistics network for fresh agricultural products (FAPs) e-commerce under the new origin e-commerce model. Compared to previous research, it specifically addresses the continuous and non-uniform character of orders and optimizes the departure time of vehicles. The objective is to reduce consumer waiting time costs, FAPs' quality loss costs, and logistics-related costs. We proposed a customized heuristic algorithm to solve the model and determined through numerical testing that the logistics plan with the optimal departure time is better than the fixed departure time logistics plan. Furthermore, comprehensive sensitivity analyses demonstrate that adjusting key cost parameters within feasible thresholds can offset their individual impacts on total cost, thereby maintaining cost stability. Logistics efficiency can only be constantly improved to lower time penalty costs, since it is more difficult to reduce costs connected to customer time satisfaction by coordinating other expenditures.</p>