With the shortage of fossil energy, more attention is paid to two-phase flow due to the high heat transfer efficiency and uniform surface temperature. However, flow distribution in parallel channels is more complex than that of single-phase flow, which usually leads to heat transfer deterioration. Thus, a 3D numerical model of flow distribution and heat transfer of two-phase flow in parallel channels is developed and validated in the present study. The effect of channel cross section was investigated, and three typical cross section shapes are discussed. The results show that the flow distribution in parallel channels of the triangular cross section is the worst, and of the circular section is the best. Similarly, the heat transfer performance of the circular channel is the best because the bubbles are difficult to separate at the junction of adjacent channel surfaces in the rectangular and triangular channel. Besides, flow distribution in the U-type heat exchanger is better than that in the Z-type heat exchanger.