In recent years, drone delivery has become one of the most widely adopted emerging technologies. Under the current Covid-19 pandemic, drones greatly improve logistics, especially in rural areas, where inefficient road networks and long distances between customers reduce the delivery capacity of conventional ground vehicles. Considering the limited flight range of drones, charging stations play essential roles in the rural delivery system. In this study, we utilize simulation to optimize the drone delivery system design, in order to minimize the cost of serving the maximum capacity of customers. As facility siting is usually difficult to optimize, we propose a novel simulation-heuristic framework that continuously improves the objective to find near-optimal solutions. In addition, we conduct a case study using real-world data collected from Knox County, Tennessee. The results suggest that the proposed approach saves over 15% on total costs compared with the benchmark.