A lot of previous research have proposed various frameworks and algorithms to optimize routes to reduce the total transportation cost, which accounts for over 70% of overall logistics cost. However, it is very hard to find the cases applied the mathematical models or algorithms to the practical business environment cases, especially daily operating logistics services like convenient stores. Most of previous research have considered the developing an optimal algorithm which can solve the mathematical problem within the practical time while satisfying all constraints such as the capacity of delivery and pick-up, and time windows. For the daily pick-up and delivery service like supporting several convenient stores, it is required to consider the unit transporting container as well as the demand, capacity of trucks, traveling distance and traffic congestion. Especially, the reusable transporting container, trays, should be regarded as the important asset of logistics center. However, if the mathematical model focuses on only satisfying constraints related delivery and not considering the cost of trays, it is often to leave the empty trays on the pick-up points when there is not enough space in the track. In this research, it has been proposed to build the mathematical model for optimizing pick-up and delivery plans by extending the general vehicle routing problem of simultaneous delivery and pickup with time windows while considering left-over cost. With the numerical experiments, it has been proved that the proposed model may reduce the total delivery cost. It may be possible to apply the proposed approach to the various logistics business which uses the reusable transporting container like shipping containers, refrigerating containers, trays, and pallets.