Microchannel flow boiling is one of the most effective solutions to the problem of heat dissipation caused by high power electronic devices. However, inherent drawbacks such as low critical heat flux due to dry-out of the liquid film near the channel exit, relatively high two-phase flow pressure drop, severe temperature nonuniformity and boiling instability at high heat flux still prevent widespread commercial application. In this study, based on the idea of uniform vapor quality along the flow direction, a copper Counter-Flow Interconnected Microchannel (CFIM) was proposed to address the main issues currently faced by two-phase microchannel heat sink. A comprehensive comparative study of CFIM, Co-Current Microchannel (CCM) and Counter-Flow Microchannel (CFM) was carried out from the aspects of boiling stability, boiling heat transfer characteristics and temperature uniformity. Three slots of 0.2 mm, 0.5 mm and 0.8 mm in width, denoted as IM0.2, IM0.5 and IM0.8, respectively, are considered. Experiments are conducted at mass fluxes of 291–618 kg/m2·s, saturation temperature of 40 °C and effective heat fluxes of 3–293 W/cm2, using the dielectric fluid R1233zd(E) as the working fluid. The results show that the CHF and average two-phase heat transfer coefficient (HTC) of CFIM are increased by 40.6 ∼ 100.5 % and 70.4–83.6 %, respectively, while the two-phase pressure drop is decreased by 17–32.6 % compared to CCM. The design of the counter-flow interconnected structure can manipulate the void fraction and two-phase flow pattern, resulting in a near uniform void fraction and flow pattern. The structure of these connecting slots promotes nucleate boiling and fluid mixing of neighboring channels. More importantly, the flow boiling instability and temperature non-uniformity in CFIM are well suppressed. In addition, IM0.2 has higher heat dissipation than IM0.5 and IM0.8 due to enhanced bubble nucleation, reducing superheat requirements and periodic rewetting to the center of the channel. The results of this research reveal that utilizing a microchannel heat sink with a counter-flow interconnected configuration can effectively improve heat transfer performance during flow boiling. Furthermore, it helps to mitigate issues such as flow boiling instability and temperature non-uniformity.