A novel heat exchanger using parallel refrigerant mini-channels has recently been developed to improve the performance of air conditioning systems. In the evaporator, due to unequal heat load among the parallel channels, boiling flow tends to be unevenly distributed. Since this phenomenon sometimes causes deterioration of heat exchange performance, it is important to clarify the characteristics of boiling heat transfer under the unequally heated condition. In the present study, a simulation model which predicts flow boiling heat transfer performance of a refrigerant heated unequally among parallel mini-channels has been developed, and simulation for two-parallel channels were carried out. Based on the calculation results, the effect of the inequality in wall temperatures between the channels on the heat transfer rate to the refrigerant was discussed. The channel mean heat transfer rate decreased with expanding the difference of wall temperatures between the channels and the deterioration rate became significant at a high mass flow velocity.