In this article, a microchannel thermal management system (MTMS) with the two-phase flow using the refrigerant R1234yf with low global warming potential is presented. The thermal test vehicles (TTVs) were made of either single or multiple thermal test chips embedded in the substrates, which were then attached to the MTMS. The system included two identical aluminum microchannel heat sinks (MHSs) connected in series in the cooling loop, which also consisted of a gas flowmeter, a miniature compressor, a condenser, a throttling device, and accessory measurement components. The experimental results showed that the thermal management system could dissipate a heat flux of 526 W/cm2 while maintaining the junction temperature below 120 °C. For SiC mosfet with a higher junction temperature, e.g., 175 °C, the current system is expected to dissipate a heat flux as high as about 750 W/cm2. The effects of the rotational speed of the compressor, the opening of the throttling device, TTV layout on MHS, and a downstream heater on the cooling performance of the system were analyzed in detail. The study shows that the present thermal management with a two-phase flow system is a promising cooling technology for the high heat flux SiC devices.