A compact silicon based manifold microchannel heat sink with embedded SiNWs was designed and fabricated in order to enhance heat transfer and reduce flow instability during two phase flow boiling. The manifold microchannel device comprises parallel longitudinal microchannels etched in a silicon substrate and transverse microchannels etched on a glass cover. Flow boiling characteristics with deionized water in such SiNWs embedded manifold microchannels were investigated. Experimental results of the SiNWs embedded device show good improvements in heat transfer performance and reduced pressure loss compared with the plain wall device. The effects of mass flux and subcooled inlet temperature were studied, and a maximum heat flux of about 431 W/cm2 has been achieved by employing different experimental conditions while confined by the capability of heating elements. Wall temperature fluctuation and flow pattern results present the effective flow instability control and dry out prevention with the capillary driven three-dimensional flow.