A three-dimensional numerical study on two-phase flow boiling is conducted for raccoon and straight microchannels. The effect of flow boiling instability is observed under conjugate conditions with water as coolant. Bubble coalescence in bubble dynamics is carefully studied, and the forces acting are identified. Eotvos and Weber number are calculated to determine the bubble behavior and shape in a raccoon microchannel. Boiling number is also considered to predict the two-phase flow boiling heat transfer. The bubble flow pattern for two-phase boiling in straight and raccoon microchannel are investigated under different parameters such as Waviness (γ∼0 - 0.267) and Mass flux (G ∼ 118 – 590 kg/m²s), keeping saturation temperature constant at T_sat = 310 K corresponding to pressure (p sat = 6500 pa). It is observed that the Eotvos and Boiling numbers are comparatively higher for values of waviness 0 – 0.067 than other raccoon microchannels. This happens due to the presence of long elongated bubbles, causing the flow boiling instability. On the other hand, as the waviness increases, the bubble size changes periodically. Effect of forces on bubble coalescence for different waviness and mass flux is also observed.