This paper develops a parametric level set-based topology optimization method for the micro-channel heat sink design. In this study, the optimal objective functional is formulated as a bi-objective functional consisting of heat transfer maximization and pressure drop minimization based on the two- and three-dimensional steady-state Navier–Stokes and energy balance equations. The normal velocity of the interface propagation, which is derived from the steepest descent method and adjoint variable method, is used to drive the evolution of the level set function. Influence of the governing equations on the optimized heat sink structure and the distribution characteristics of adjoint variables are analysed through numerical experiments, which proved that governing equations can improve the heat dissipation capacity of the optimal structure. Based on Earth Mover’s Distance, the developed method is proved to have less dependence on initial structures compared with the density-based topology optimization method. Finally, through the experimental tests and numerical simulations, the effectiveness of the developed model is confirmed.