A three-dimensional numerical study has been carried out to understand the effect of axial wall conduction in a conjugate heat transfer situation in a wavy wall square cross section microchannel engraved on solid substrate whose thickness varying between 1.2-3.6 mm. The bottom of the substrate (1.8 × 30 mm2) is subjected to constant wall heat flux while remaining faces exposed to ambient are assumed to be adiabatic. The vertical parallel walls are considered wavy such that the channel cross section at any axial location will be a square (0.6 × 0.6 mm2) and length of the channel is 30 mm. Wavelength (λ) and amplitude (A) of the wavy channel wall are 12 mm and 0.2 mm respectively. Simulations has been carried out for substrate thickness to channel depth ratio (δsf ∼ 1 - 5), substrate wall to fluid thermal conductivity ratio (ksf ∼ 0.34 -646) and flow rate (Re ∼ 100 to 500). The results show that with increase in flow rate (Re), the hydrodynamic and thermal boundary layers are thinned due to wavy passage and they shifted from the centerline towards the peak which improves the local heat transfer coefficient at the solid-fluid interface. It is also found that after attaining maximum Nuavg at optimum ksf, the slope goes downward with increasing ksf for all set of δsf and flow rate (Re) considered in this study. © 2016 by ASME.