Typically, the flow through a microchannel network of a lab-on-a-chip device is viscous dominant. Concomitantly, the fluid transport is laminar and the intermixing of fluid layers is absent. Thus, it becomes a challenging task to rapidly homogenize different species within the limited spacial region available. In this context, to enhance the micro-mixing, we extend the work of Ranjith et al. [Soft Matter (2014), Microfluid. Nanofluid. (2015)] who suggested that a sudden drift in wall shear stress generates cross-stream momentum. Such microchannels are realized by periodically coating a hydrophilic wall with hydrophobic materials by keeping the orientation of these regions in the transverse direction to the pressure gradient. In the present study, the computational fluid dynamics is employed to investigate the convective mixing in Y-mixers decorated with such hybrid hydrophobic-hydrophilic surfaces. These microchannels are considered as a combination of several alternately repeating hydrophobic and hydrophilic patches which indeed modeled as an agglomeration of no-slip and partial-slip surfaces. Here, the improvement in mixing owing to the churning of species inside these channels in comparison with conventional hydrophilic confinement is examined in detail. We observed that, the lateral velocity generated throughout stripped channel promotes homogenization in comparison with its uniformly hydrophobic counterpart. In addition to that, the presence of hydrophobic surfaces reduces the hydrodynamic resistance offered by the channel, which in turn saves the pumping power significantly.