To investigate the effect of the target weight coefficient on the structure design of the micro-channel heat sink, an innovative method for the topology optimization design of micro-channel structures with different bifurcation angles is adopted. In this study, the improved interpolation function, density filtering, and hyperbolic tangent projection methods are adopted to obtain a clear topological structure of the micro-channel heat sink. The heat transfer of the micro-channel heat sink under different bifurcation angles is compared. At the same time, the influence of the two different objective functions, heat transfer, and flow energy consumption, is analyzed in the topology optimization of micro-channel heat sinks. The results show that when the bifurcation angle is 135°, both the heat transfer and the average outlet temperature of the micro-channel heat sink obtain the maximum value, and the heat transfer effect is the best. With the increase of the heat transfer weighting coefficient, the distribution of solid heat sources in the main channel increases, and the refinement of the branch channels also increases. On the other hand, although the heat transfer effect of the micro-channel heat sink is the best, the corresponding flow energy consumption is larger.