Three-dimensional numerical study on two-phase flow boiling in rectangular microchannel with wavy vertical wall configuration is considered that can be utilized for heat dissipation in high flux electronics devices. Straight and wavy microchannels are considered for comparison and analysis. Under conjugate heat transfer situation, effect of flow boiling instability in straight and wavy microchannel is numerically studied using water as the working fluid. Behaviour of bubble growth rate and two-phase flow pattern in straight and wavy microchannel are investigated for a wide range of parameters such as waviness (γ ~ 0 - 0.267), substrate thickness to channel height ratio (δsf ~ 1 and 5), wall to fluid conductivity ratio (ksf ~ 22 - 646), and mass flux (G ~ 118 - 590 kg/m2s). It is found that smaller bubbles are formed in wavy microchannel while confined and elongated bubbles are formed in straight microchannel which often causes flow clogging and premature dryout. The work also presents a comparative analysis between single-phase and two-phase flow boiling cooling technique in straight and wavy microchannel under same geometrical parameters and applied heat flux. © 2020