For microfluidic systems, interfacial phenomena in micro-reactors are of great importance because they control the transfer and reaction characteristics. This paper dwells on how the surface property and geometry influence the mass flux in a complex microchannel. The lattice Boltzmann method(LBM) with a pseudo potential model and the Shan–Chen model for the interaction between fluid and hydrophobic surface were built up, so a boundary slip effect was added and verified. On this basis, a microchannel with variable-section geometry was simulated. The results indicate that the optimal design and the flow pattern are quite different under hydrophilic and hydrophobic conditions. A microchannel with sequential hydrophilic and hydrophobic surface was also simulated. The numerical results indicate that the hydrophobic wall can improve the mass flux, irrespective of microchannel geometry. Particularly, an empirical correlation with a linearly relationship between length of hydrophobic segment and mass flux was obtained for the straight microchannel. For microfluidic systems, interfacial phenomena in micro-reactors are of great importance because they control the transfer and reaction characteristics. This paper dwells on how the surface property and geometry influence the mass flux in a complex microchannel. The lattice Boltzmann method (LBM) with a pseudo potential model and the Shan-Chen model for the interaction between fluid and hydrophobic surface were built up, so a boundary slip effect was added and verified. On this basis that a microchannel with variable-section geometry was simulated. The optimal design and the flow pattern are quite different under hydrophilic and hydrophobic conditions. A numerical result indicates that the hydrophobic wall can improve the mass flux, irrespective of microchannel geometry. Particularly, an empirical correlation with a linearly relationship between length of hydrophobic segment and mass flux was obtained for the straight microchannel.