In this paper, a new experimental setup was proposed to realize the constant-heat-flux boundary condition based on a counter flow microchannel heat exchanger with the same heat capacity rate of the hot and cold streams. This approach provides a constant fluid temperature gradient along the surfaces. An analytical two-dimensional model was developed to describe the heat transfer processes in the hot stream and the cold stream, respectively. In the experiments, DI-water was employed as the working fluid. Laser induced fluorescence (LIF) method was used to measure the fluid temperature field within the microchannel. Different combinations of flow rates were studied to investigate the heat transfer characteristics in the microchannel. The measured mean temperature distribution matched well with the proposed analytical model. A correlation for Nusselt number (Nu) was proposed based on the experimental Reynolds number (Re < 1) and Prandtl number (Pr).