To achieve efficient air conditioning of data centres, we constructed a spot cooling-type carbon dioxide heat transportation system for servers on the basis of typical data centre air-conditioning techniques. In previous studies, we investigted the operational characteristics of forced and natural circulation methods under the condition of two-phase flow between server racks, with carbon dioxide as the working fluid. In this paper, we focused on a sudden unsteady variation in variables such as temperature and flow rate that may cause heat transportation in this system to become unstable. Here we construct a mathematical model and investigate the transient operational characteristics of heat transportation with two-phase flow in the unsteady state through simulations and experiments. Factors such as the server room temperature and cooling water temperature were considered as key variables that influence the heat transfer characteristics of the condenser and evaporator. The results showed that the experimental and simulated effects of air temperature and cooling water temperature were almost consistent. We also clarified the transient characteristics of the heat transportation system with carbon dioxide as the working fluid.