Flow boiling in microchannel heat sinks is an efficient way to dissipate high heat flux by utilizing the large surface-to-volume ratio and high latent heat. Previous studies of boiling heat transfer in microchannels mainly consider the fluid flow in channels only, but often neglect the conjugate effects of the heat conduction in the solid wall, which becomes important for microchannels because of the comparable sizes of the flow channel and the solid wall. In the present study, the effects of conjugate heat transfer on bubble growth during flow boiling in microchannels are examined by numerical simulation. The results indicate that the bubble growth is non-uniform for different bottom wall thicknesses or different solid materials even with the same heat flux at the wall. As the bottom wall thickness increases, the bubble growth rate increases because of the heat conduction in the solid wall along the channel direction. The increased bubble size also increases the perturbation to the flow field, and enhances the thermal convection between the fluid and the wall. For different solid materials, the high-thermal-diffusivity material possesses a higher heat transfer performance because of the quick diffusion of thermal energy from the heat source to the solid–fluid interface.