The low efficiency of cooling equipment is an important factor in the high energy consumption of data center cooling systems. An advanced model predictive control (MPC) strategy is proposed for the efficient operation of cooling equipment in a water-storage hybrid-free cooling system. The control effectiveness of MPC in different climate zones is evaluated. In addition, taking Guangzhou as an example, the influence of equipment deterioration on control performance is analyzed. The results show that the proportion of mechanical cooling time determines the extent of PUE reduction in different cities, and the order of decrease in annual PUE from large to small in Guangzhou, Changsha, Beijing, Harbin, and Kunming. The influence degree of equipment performance deterioration on PUE from large to small is chiller, chilled water pump, cooling water pump, cooling tower, and cooling pump. The effect of cooling tower approach temperature on PUE is higher than that of heat exchange.