To enhance the heat transfer efficiency of multiple flow-passage heat exchangers (MFHE) used in various industrial fields, it is very important to evenly distribute the working fluid in each flow passage. The flow distribution of multiphase fluids has been mostly studied experimentally thus far because of its phenomenological complexity. In this study, a direct numerical analysis of the flow distribution of the liquid-vapor two-phase refrigerant in MFHEs was conducted. The two-phase flow distribution through the branched multiple microchannels was numerically simulated by using volume of fluid (VOF) interface tracking method. The proposed numerical procedure was successfully verified through comparison with prior experimental results for a horizontal header with 10 vertical branch tubes. The results showed satisfactory agreement. The intermittent inflow of liquid into the microchannels was revealed to play an important role in enhancing the two-phase flow distribution and preventing flow clogging in the microchannels.