The micro structured surfaces have significant impact on the flow patterns and heat transfer mechanisms during the flow boiling process. The hydrophobic surface promotes bubble nucleation while the hydrophilic surface supplies liquid to a heating surface, thus there is a trade-off between a hydrophobic and a hydrophilic surface. To examine the effect of heterogeneous wetting surface on flow boiling process, an experimental investigation of flow boiling in a rectangular vertical narrow microchannel with the heterogeneous wetting surface was conducted with deionized water as the working fluid. The heat transfer characteristics of flow boiling in the microchannel was studied and the flow pattern was photographed with a high-speed camera. The onset of flow boiling and heat transfer coefficient were discussed with the variation of heatfluxes and mass fluxes, the trends of which were analyzed along with the flow patterns. During the boiling process, the dominated heat transfer mechanism was nucleate boiling, with numerous nucleate sites between the hydrophilic/hydrophobic stripes and on the hydrophobic ones. In the meantime, after the merged bubbles were constrained by the channel walls, it would be difficult for them to expand towards upstream since they were restricted by the contact line between hydrophilic/hydrophobic stripes, thereby reduce the flow instability and achieve remarkable heat transfer performance.