This study aims to explore the heat transfer characteristics of flow boiling in the minichannels under the action of phase separation structure. A test section of parallel counterflow minichannel was also fabricated with the different structures of phase separation. Furthermore, the pressure difference between the downstream and counterflow channel confined the bubbles to discharge the gas phase from the high- to the low-pressure channel through the phase separation film. The gas phase separation was realized under the high- and low-pressure switching between adjacent channels. Two kinds of structure channels were fabricated:Type 1 phase separation structure channel (SPS1 channel) (Structure of Phase Separation, SPS) with few vents, and type 2 phase separation structure channel (SPS2 channel) with multiple vents, compared with the SPS3 channel without phase separation structure. The aqueous glycerol solution with a mass fraction of 30% was used as the test working medium. The flow boiling test was performed on the rectangular minichannel with a cross-section of 2 mm×2 mm under the effective heat flux density is 151.43 kW/m², the mass flow rate of 121.25 kg/(m²·s), and inlet temperature of 70℃. A systematic investigation was made to clarify the effects of high- and low-pressure switching cycles on the comprehensive performance and phase separation structures on the flow boiling heat transfer and temperature uniformity in minichannels. A high-speed camera was used to determine the length-to-diameter ratio of confined bubbles and the gas phase separation. An analysis was made to explore the heat transfer enhancement of the minichannel flow boiling under the action of the phase separation structure. The results show that the local saturated boiling heat transfer coefficient was the highest, and the total pressure drop was the lowest when the high- and low-pressure switching cycle was 120 s under the experimental conditions. An optimal value was achieved in the high- and low-pressure switching cycle. There was little difference in the boiling curve before the ONB point, while after the ONB point, the wall superheat of SPS2 and SPS3 channels was lower at the same heat flux. The maximum coefficients of local saturation boiling heat transfer in the SPS2 and SPS3 channels increased by 18.87% and 26.65%, respectively, compared with the SPS3. More importantly, the temperature uniformity of the SPS2 channel was the best in the two-phase region, SPS1 was the second, and SPS3 was the worst. The wall temperature standard deviations were reduced by 10.81% and 18.91%, respectively, along the SPS1 and SPS2 channels. The visual analysis results show that the phase separation structure reduced the length-to-diameter ratio of the confined bubbles, leading to the flow pattern transformation in the channel. Enhanced heat transfer was achieved in the first half cycle of the high- and low-pressure switching cycle. The length-to-diameter ratios of confined bubbles in the SPS1, SPS2, and SPS3 downstream channels were −118.71%, −158.16%, and 122.45% in the unit time, respectively. The phase separation structure can be expected to effectively enhance the heat transfer performance of flow boiling, and then improve the temperature uniformity of minichannels. The finding can provide new ideas for the application of the phase separation structure in minichannel heat exchangers.annel heat exchangers.