We present a combined numerical and experimental study of a novel design for a vortex-based mixer by virtue of easy insertion of inlet tubes into a capillary-based square channel. We show that, as the Reynolds number (Re) increases above 72, different patterns of vortices develop by changing the inlet configuration. At relatively higher Re, we observe that the disturbance posed by a vortex on the contact surface is not only dependent on its vorticity, but also correlates with the direction of vortex/vortex pair. As a consequence, recognition and application of suitable vortex pattern is of great importance for mixing enhancement. The designed mixer under four inflow confluence conditions, producing single vortex or vortex pair with different directions, shows different mixing performance in the Re range from 20 to 280, from which the optimum design approach capable of generating counter-rotating vortex pair along the outflow direction with higher mixing quality is found. This explains the mass transport and mixing observed in fluid flows with a vortex, which to date has not been studied before.