In this study, computational fluid dynamics (CFD) analysis was performed to investigate the cause of the thermal stratification in the channel and the temperature non-uniformity of the plate heat exchanger. The flow velocity maldistribution of the channel and the merging parts caused temperature non-uniformity in the channel width direction. The non-uniformity of flow velocity and temperature in the channel is shown in Section 1 > Section 3 > Section 2 from the heat exchanger. The non-uniform temperature distribution in the channel caused channel stratification and non-uniform outlet temperature. Stratification occurred at the channel near the merging due to the flow rate non-uniformity in the channel. In particular, as the mass flow rate increased from 0.03 to 0.12 kg/s and the effectiveness increased from 0.436 to 0.615, the cold-side stratified volume decreased from 4.06 to 3.7 cm3, and the temperature difference between the stratified area and the outlet decreased from 1.21K to 0.61K. The increase in mass flow and the decrease in temperature difference between the cold and hot sides alleviated the non-uniformity of the outlet temperature due to the increase in effectiveness. Besides, as the inlet temperature difference between the cold and the hot side increases, the temperature non-uniformity at the outlet port is poor due to the increase in the stratified region at the channel, and the distance to obtain a uniform temperature in the outlet pipe increases as the temperature at the hot side increases.