Abstract Cross flow heat exchangers are important components used in data center cooling systems. The thermal environment usually becomes very complex due to the cooling system design configuration, including individually operated IT equipment inside the data center. Nonuniform fluid inlet temperature conditions may become very common in the cross flow heat exchangers, and may impact the performance of these heat exchangers. In this study, cross flow heat exchanger performance is investigated accounting for the nonuniform input effect of fluid inlet temperature. Several types of nonuniform inlet temperature boundary condition model are developed, based on the several actual problems in data center thermal management. The detailed effect of these nonuniform temperature boundary conditions on both the steady state and transient responses of a crossflow heat exchanger are investigated. The combined effects of the physical model parameters with nonuniform temperature boundary conditions are also analyzed. Several specific cases related to the practical application situations of cross flow heat exchangers and thermal management in data centers are outlined and analyzed in this study.