In this paper, conjugate heat transfer in a wavy walls microchannel with different geometrical parameters has been studied numerically to find the optimum geometry with maximum Nusselt number. A constant heat flux boundary condition has been applied on the bottom wall of the micro-device. Water used as working fluid and the body is made of silicon. Due to wavy boundaries, a body fitted mesh has been used. Then three-dimensional governing equations including continuity, Navier–Stokes and energy have been discretized using the finite-volume method. Then, they have been solved by the well-known SIMPLE method in a curvilinear coordinate system with the collocated grid. Effects of geometrical parameters including aspect ratio, wall thickness, amplitude and wavelength have been investigated. Numerical results show that the Nusselt number in wavy microchannel is more than that for flat walls microchannels. Also in opposite of flat walls microchannels there is an optimum geometry for wavy walls microchannels, which has the maximum Nusselt number.