In order to develop high-efficiency low-resistance heat exchangers, the heat transfer performance and further optimization of water-cooled microchannel heat sink with dimple and pin-fin were numerically studied in this work. Firstly, the combination effects of structure parameters (diameter of pin-fin D-1, depth of dimple delta and stream-wise spacing S) on flow structure and heat transfer were investigated in detail. The results show that the proposed designs exhibit heat transfer augmentation with energy saving and low-resistance features. The increase of D-1 and decrease of S bring out the increase of Nu/Nu(0) under all Re studied. Flow structures induced by pin-fin make the development of separation flow in the dimple happened in advance. The increase of D-1 enlarges the scale and intensity of wake flow of pin-fin, resulting more violent actions of flow on heated walls, then, enhances the heat transfer augmentation. Also, relative small delta will be beneficial for heat transfer enhancement at lower Re conditions. Furthermore, the automatic calculation configuration optimization analysis by means of pattern search method was validated and conducted successfully to achieve better TP, and the maximum increasement of TP, 10.3%, is obtained at Re = 200 as a result. The area of high temperature regions, especially on the side walls, decreases, also, the temperature gradient decreases and the uniformity of heated walls is enhanced. The proposed method can be extended to optimize configuration of microchannel with flow control devices accurately with less time-consuming. (C) 2017 Elsevier Ltd. All rights reserved.