Summary: A full 3-dimensional (3D) conjugate heat transfer model has been developed to simulate the heat transfer performance of silicon-based, parallel microchannel heat sinks. A semi-normalized 3-dimensional heat transfer model has been developed, validated and used to optimize the geometric structure of these types of microheat sinks. Under a constant pumping power of 0.05 W for a water-cooled microheat sink, the optimized geometric parameters of the structure as determined by the model were a pitch of 100 \(\mu m\), a channel width of 60 \(\mu m\) and a channel depth of about 700 \(\mu m\). The thermal resistance of this optimized microheat sink was calculated for different pumping powers based on the full 3D conjugate heat transfer model and compared with the initial experimental results obtained by Tuckerman and Pease in 1981. This comparison indicated that for a given pumping poser, the overall cooling capacity could be enhanced by more than 20% using the optimized spacing and channel dimensions. The overall thermal resistance was 0.068 \(^\circ C/W\) for a pumping power of 2 W.