This study investigated an interconnected microchannel (IMCHS) thermal management system using the flow boiling of HFE-7100, focusing on enhanced heat transfer by confining a two-phase mixture within the IMCHS. The interconnection channels were designed to promote continuous thermal boundary layer disruption and improve mixing, facilitating the exploration of suitable microchannel geometry. Contour plots were utilized to visualize key flow phenomena, with attention given to the instabilities induced by the interconnectors, as indicated by local non-dimensional fluctuations in pressure, temperature, and velocity fields. Six different geometric configurations were analyzed and compared with conventional parallel microchannels by varying the width and location of interconnectors, while maintaining a constant aspect ratio of 1. Four distinct mass fluxes (280.4, 560.8, 841.2, and 1121.6 kg/m2s) were applied in counterflow, along with a constant heat flux of 40 W/ cm 2 at the sink bottom, to assess the thermal and hydraulic performance. Key parameters, such as pressure drop penalty, Nusselt number, thermal resistance, and total vapor fractions, were evaluated at varying mass fluxes. The performance analysis revealed a maximum reduction in pressure drop penalty of around 30 % at 560.8 kg/ m2s. Moreover, a significant improvement in the Nusselt number (approximately 34 %) and a reduction in thermal resistance (about 23 %) were observed at 1121.6 kg/m2s. These improvements in thermal and hydraulic performance enabled effective dissipation of high heat fluxes while reducing the pumping power requirement, providing a guideline for future design.