The loading of heat transfer exchanger is increased with the development of technology and the increasing demand of energy. In order to improve the efficiency of compact heat exchanger and microchannel heat sinks, flow and heat transfer characteristics of Al2O3-water nanofluids in the microchannel with dimple and protrusion surface are investigated for the first time. The effects of nanoparticle volume fraction phi (0-3%), inlet velocity U(1.2-8.7 m s(-1)) and geometrical structure of microchannel on flow and heat transfer characteristics are studied in detail. Three similar microchannel structures are adopted in the present work, which were smooth, dimpled and dimpled + protrusioned microchannel. The results show that the relative Fanning friction factor f/f(0), Nusselt number Nu/Nu(0) and thermal performance TP increase with the increase of U for nanofluids. The flow structures change obviously as phi increases for the fixed microchannel structure and U. Flow separation and reattachment in the dimple does not contain two symmetrical focuses or single focus any more when U and phi are larger, and the locations of separation and reattachment show the trend of drawing close, so the size of separation bubble decreases. Moreover, in the microchannel with staggered dimple and protrusion, the asymmetric flow pattern is weakened. Meanwhile, average wall temperature decreases with the increase of phi, indicating heat transfer augment is obtained. From the analysis of performance evaluation plot, the proposed cases are energy saving. Furthermore, the effects of U and geometrical structure on the flow field and heat transfer performance are weakened due to the introduction of nanofluids in the microchannel heat sinks. (C) 2014 Elsevier Ltd. All rights reserved.