Maldistribution seriously impacts the heat transfer performance of the microchannel heat exchanger (MCHX). Fully understanding the two-phase distribution in the heat exchanger is important for advancing academic research and engineering applications. This study introduces a novel method for quantifying two-phase distribution in a microchannel heat exchanger. An experimental setup was developed to measure the local vapor mass fraction in the heat exchanger header. Capacitance signals were measured under inlet vapor mass fractions from 0 to 1, and inlet flow rates of 10, 15, and 25 g s−1 corresponding to a mass flux of 17.47, 26.2, and 43.66 kg m−2s−1, respectively. The local vapor mass fraction in the header was estimated using the capacitance measurements. The mass flow rate in the header, the microchannel tube, and the vapor mass fraction in the tube were calculated using the proposed model. The calculation model was validated against literature data, and the results were analyzed. The analysis reveals the characteristics of vapor mass fraction and mass flow rate distribution in the MCHX and further elaborates on the effects of phase separation, entrainment ratio, and pressure drop balance on the distribution. The proposed method can evaluate distribution in the header and tubes of microchannel heat exchangers, and it is also applicable to other types of two-phase flow devices.