Flow boiling in a microchannel without or with surface modifications, such as fins, grooves, and cavities, has received significant attention as an effective cooling method for high-power microelectronic devices. However, a general predictive approach for the boiling process has not yet been developed because of its complexity involving the bubble dynamics coupled with boiling heat transfer in a microscale channel. In this study, direct numerical simulations for flow boiling in a surface-modified microchannel are performed by solving the conservation equations of mass, momentum, and energy in the liquid and vapor phases. The bubble surfaces are determined by a sharp-interface level-set method, which is modified to include the effect of phase change at the liquid-vapor interface and to treat the no-slip and contact-angle conditions on immersed solid surface of microstructures. This computation demonstrates that the surface-modified microchannel enhances boiling heat transfer significantly compared to a plain microchannel. The effects of various surface modifications on the bubble growth and heat transfer are investigated to find better conditions for boiling enhancement.