Flow boiling in microchannel heat sink offers an effective cooling solution for high power density micro devices. A three-dimensional numerical study based on volume of fraction model (VOF) coupled with evaporation condensation model accounting for the liquid-vapor phase change is undertaken to recreate vapor bubble formation in saturated flow boiling in wavy microchannel. Constant wall heat flux imposed at the bottom surface of the substrate while other faces are insulated. To understand the conjugate effects, simulations has been carried out for substrate thickness to channel depth ratio (δsf ~ 1 - 5), substrate wall to fluid thermal conductivity ratio (ksf ~ 22 - 300) and waviness (γ ∼ 0.008 -0.04). Bubble nucleation, growth, and departure of bubble plays a significant role in heat transfer and pressure drop characteristics in two-phase flow in wavy microchannel. The coolant (water) temperature at the inlet is taken to be 373 K while flow was at atmospheric pressure. This makes shorter waiting period of bubble nucleation, and the number density of bubbles on the solid surface increases. This results in enhancement of the boiling effect, and thus with the presence of bubbles, the mixing of laminar boundary layers improves and enhances the overall heat transfer coefficient. Channel amplitude play an important factor that can suitably reduce the friction factor and enhances the heat transfer coefficient. Copyright © 2018 ASME.