This study aims to explore the flow boiling heat transfer characteristics in the minichannels under the action of phase separation structure, a parallel counterflow minichannel test section with different phase separation structures was fabricated in this paper. There is a pressure difference between the downstream channel and the counterflow channel, and confined bubbles discharge the gas phase from the high pressure channel to the low pressure channel through the phase separation film. The gas phase separation is realized by the high and low pressure switching between the adjacent two channels. Two kinds of phase separation 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, which were compared with SPS3 channel without phase separation structure. The aqueous glycerol solution with a mass fraction of 30% was used as the test working medium, and 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 ranges from 23.68 kW/m2 to 151.43 kW/m2, the mass flow rate of 121.25 kg/(m2·s), and the inlet temperature of 70°C. Study the effects of high and low pressure switching cycles on the comprehensive performance and different phase separation structures on the flow boiling heat transfer characteristics and temperature uniformity in minichannels. A high-speed camera was used to investigate and analyse the change of the length-to-diameter ratio of confined bubbles and the gas phase separation, the heat transfer enhancement mechanism of the minichannel flow boiling under the action of the phase separation structure was analyzed. The results show that under the experimental conditions, the local saturated boiling heat transfer coefficient is the highest and the total pressure drop is the lowest when the high and low pressure switching cycle is 120 s, there is an optimal value of the high and low pressure switching cycle. There is little difference in the boiling curve before the ONB point, while after the ONB point, the wall superheat of SPS2 and SPS3 channels is lower at the same heat flux. The maximum coefficients of local saturation boiling heat transfer of the SPS2 channel and SPS3 channel are increased by 18.87% and 26.65%, compared with the SPS3 channel. In the two-phase region, the temperature uniformity of SPS2 channel is the best, SPS1 is the second, and SPS3 is the worst. The wall temperature standard deviation along the way of SPS1 channel and SPS2 channel are reduced by 10.81% and 18.91%. The visual analysis results show that the phase separation structure can reduce the length-to-diameter ratio of the confined bubbles and affect the flow pattern transformation in the channel, so as to achieve the purpose of enhanced heat transfer. In the first half cycle of the high and low pressure switching cycle, the change of length-to-diameter ratios of confined bubbles in SPS1, SPS2 and SPS3 downstream channels are-119% s-1, -157% s-1 and 122% s-1 in unit time, respectively. The above studies show that the phase separation structure can effectively enhance the flow boiling heat transfer performance and improve the temperature uniformity of minichannels, which may provide new ideas for the application of the phase separation structure in minichannel heat exchangers.