With the rapid development of microelectromechanical systems (MEMS) in IT industry, the heat flux in microchannel has reached a high level which demands preferable cooling technology. Water cooling has become a favor cooling approach in electronic microdevices due to better thermal performance than air cooling method. In the present paper, thermal performance in microchannels with grooves and obstacles are investigated numerically. The height and width of the rectangular microchannel are 200 and 50 μm, respectively. As a simple modification of dimple/protrusion, the groove/obstacle diameter is 100 μm and the depth is 20 μm. Different arrangements of grooves and obstacles are considered on Reynolds range of 100–900. The numerical results show that groove/obstacle structure is effective for cooling enhancement in microchannel. Among the cases in this research, the normalized Nusselt number Nu/Nu0 is within the range of 1.446–26.19, while the pressure penalty f/f0 has a much larger range from 0.86 to 110.18 depending on specific orientation. Field synergy analysis and performance evaluation plot are adopted to discuss the mechanism of heat transfer enhancement and energy saving performance integrating the pumping performance. From the viewpoint of energy saving, groove on single surface (case 1) has the best performance. Furthermore, performances of grooved microchannels are compared with that of dimpled microchannels which were discussed in the author’s previous research. The results indicate grooved microchannels have larger range of both Nu/Nu0 and f/f0 and some grooved cases possess high TP than dimpled microchannels.