This paper presents a two-phase heuristic method that can be used to efficiently solve the intractable multi-depot vehicle routing problem with time windows. The waiting time that was ignored by previous researchers is considered in this study. The necessity of this consideration is verified through an initial experiment. The results indicate that the waiting time has a significant impact on the total distribution time and the number of vehicles used when solving test problems with narrow time windows. In addition, to fairly evaluate the performance of the proposed heuristic method, a meta-heuristic method, which extends the unified tabu search of Cordeau et al., is proposed. The results of a second experiment reveal that the proposed heuristic method can obtain a better solution in the case of narrow time windows and a low capacity ratio, while the proposed meta-heuristic method outperforms the proposed heuristic method, provided that wide time windows and a high capacity ratio are assumed. Finally, a well-known logistics company in Taiwan is used to demonstrate the method, and a comparison is made, which shows that the proposed heuristic method is superior to the current method adopted by the case company.