In this paper, we designed tree-like branch structures with two levels according to generalized Murray’s law, and set them as obstacles in microchannels. The influence of the mixing performance of the micromixer was studied by changing the geometry sizes of obstacles, the branch angles and the distances between obstacles. The mixing performance of micromixer was analyzed from three aspects, including mixing efficiency, flow behavior, and pressure drop.We designed three different obstacles A, B, and C, the micromixer with obstacle C has the highest mixing efficiency. For the distances of obstacles, the micromixer with smaller distance has the higher mixing efficiency. The micromixer with branch angle of 75° has the highest mixing efficiency in the range of Reynolds number (Re) 0.1 to 150.