The aim of this paper is to propose new approaches using isolated doors to improve the efficiency of the operating system in a dangerous goods warehouse. Whether the design of isolation door is reasonable or not can be evaluated by four indicators, i.e., operational cost, time, efficiency, and safety. Technique for order preference by similarity to an ideal solution (TOPSIS)-hypercube segmentation method and hesitant fuzzy set algorithm are applied to make the evaluation more objective. Therefore, the leading innovation points are two kinds of decision-making models proposed and applied in the process of studying how to use isolation door reasonably, where the first one has no fixed indicator weight, whereas the second one has. Furthermore, the decision-making model using the isolated doors is verified by data collected from dangerous goods warehouse in Shanghai Port and 34 samples from the clients' storage capacity. The main characteristic of this paper is that with the rational use of isolated doors, the operational efficiency of stock in and stock out processes can improve as well as the logistics cost can be reduced. Finally, a comparison has been made between the proposed interconnected dangerous goods warehouse with isolated doors and the existing one, which indicates that the former one is more effective.