Due to the micro-channel size effect and thermophysical property variations, the heat transfer characteristics of S-CO2 are unclear which are crucial for the design of printed circuit heat exchanger (PCHE). This study experimentally investigated the heat-transfer phenomenon and heat-transfer coefficient of supercritical carbon dioxide (S-CO2) heated in horizontal rectangular microchannels. The effects of different parameters, including an operating pressure of 9–12 MPa, mass flow rate of 290–1200 kg/m2·s, and heat flux of 25–50 kW/m2, on the S-CO2 heat-transfer characteristics were analysed. The experimental results show that the peak value of the heat-transfer coefficient appears near the pseudo-critical point, and the peak value moves in the direction of high temperature and decreases as the operating pressure increases. Compared with the 2-mm-diameter channel, the buoyancy has a smaller effect on heat transfer in the 1-mm-diameter channel. Consequently, a new heat transfer correlation was developed wherein the microchannel size effect and thermophysical property variations are fully considered.