In this paper, conjugate heat transfer in wavy microchannels using nanofluid has been studied numerically. The nanofluid has been simulated as two-phase model using Eulerian-Lagrangian approach. Nanofluid is water-Al2O3 with 120 nm diameter and volume fraction from 0% to 2%. Three-dimensional governing equations including continuity, Navier-Stokes and energy equations have been solved by well-known SIMPLE method. The governing equations for particles have been solved by four order of Runge-Kutta. Two-ways coupling between the fluid and particles phases is employed and appears in the momentum and energy equations of fluid as source terms. The results show a good agreement with experimental results. The Nusselt number increases because of wavy walls of the microchannel in compare with straight walls microchannels and because of using nanofluid instead of water as working fluid. Also, the increase in particles volume fraction result in Nusselt number increment without sensitive increase in pressure drop. (C) 2015 The Society of Powder Technology Japan. Published by Elsevier B.V. and The Society of Powder Technology Japan. All rights reserved.