Improving flow boiling stability is crucial for ensuring the safety in fields such as thermal management and microfluidic technology. Based on vapor–liquid separation analysis, multiple-pore phase-separated configurations have been proven to effectively enhance the stability of flow boiling in mini-channels. However, these structures primarily focus on expelling vapor from the mini-channel outlet, and vapor–liquid separation between adjacent mini-channels has not been addressed. In order to enhance and quantitatively analyze the vapor–liquid separation effect of phase-separated configurations, three phase-separated configurations with porous permeable membranes are prepared and experimentally studied in counter-flow mini-channel heat sinks: multiple-pore phase-separated configuration, sparse-pore phase-separated configuration, and poreless phase-separated configuration. The study found that phase-separated configurations effectively achieve vapor–liquid separation between adjacent mini-channels, thereby improving vapor–liquid distribution within the channels. Compared to sparse-pore and poreless phase-separated configurations, the multiple-pore phase-separated configuration offers greater advantages in enhancing the flow stability of mini-channel systems. Among them, the multiple-pore phase-separated configuration shows a maximum reduction of 24.71 % in the two-phase flow pressure drop, and with the increase in heat flux, this reduction becomes more pronounced compared to the conventional poreless structure. Additionally, the vapor permeation parameter X for the multiple-pore phase-separated configuration is increased by 27.66 % compared to the sparse-pore phase-separated structure, indicating a higher vapor transfer rate per unit time for the multiple-pore phase-separated structure. Simultaneously, the potential physical mechanisms underlying the suppression of flow instability in mini-channels by phase-separated structures are discussed in this study.