Novel double-layered microchannel heat sinks with different channel geometries in each layer (Structure 2 for short) are designed to reduce pressure drop and maintain good heat transfer performance, which is compared with structure 1 (the same of complex channel geometry in each layer). The effect of parallel flow, counter flow and different channel geometries on heat transfer is studied numerically. Moreover, the essence of heat transfer enhancement is analyzed by thermodynamics. On one hand, the synergy relationship between flow field and temperature field is analyzed by field synergy principle. On the other hand, the irreversibility of heat transfer is studied by transport efficiency of thermal energy. The results show that the temperature distribution of counter flow is more uniform than that of parallel flow. Furthermore, heat dissipation and pressure drop of structure 2 are both better and lower than that of structure 1. Form the viewpoint of temperature distribution, structure C2 (i.e., counter flow with rectangular channels in upper layer and complex channels in bottom layer) presents the most uniform bottom temperature for microelectronic cooling. However, comprehensive heat transfer performance of structure P2 (i.e., parallel flow with rectangular channels in upper layer and complex channels in bottom layer) shows the best from the viewpoint of thermodynamics. The reasons can be ascribed to the channel geometry of structure P2 can obviously improve the synergy relationship between temperature and velocity fields, reduce fluid temperature gradient and heat transfer irreversibility. (C) 2017 Elsevier Ltd. All rights reserved.