The flow boiling characteristics of R32 and R1234ze(E) were investigated in a horizontal multiport tube with rectangular minichannels. The local heat transfer coefficient and frictional pressure drop were measured under mass fluxes of 50–400 kg m−2 s−1 at a saturation temperature of 15 °C. The heat transfer was characterized by forced convection in the region with a low heat flux, high mass flux, and high vapor quality; the heat transfer was characterized by nucleate boiling in the region with a high heat flux and a low vapor quality. Moreover, the heat transfer was characterized by the thin liquid film formed around the elongated vapor plugs with a low mass flux and low heat flux. These heat transfer mechanisms were also confirmed based on the visualization results of the flow boiling. The heat transfer deteriorated in the plug and slug-annular flows due to the occurrence of dry patches. A new heat transfer model for multiport rectangular minichannels was developed that considered forced convection, nucleate boiling, and thin liquid film evaporation. Moreover, this new heat transfer model considered flow patterns inside the multiport minichannels, heat transfer deterioration due to dry patches, and dryout inception quality. The newly model can predict the heat transfer characteristics in multiport rectangular minichannels for a mean deviation of less than approximately 15%. The frictional pressure drop of R32 was smaller than that of R1234ze(E) under the same mass flux and vapor quality conditions and compared with previous correlations.