A microchannel reactor improves the overall mass and heat transfer as compared with a conventional reactor. This is attributed to the creation of a high area-to-volume ratio and enhanced mixing due to the presence of the vortices inside the slug. In this paper, the mass-transfer performance was studied using a cross-junction microchannel. Subsequently, the computational fluid dynamic (CFD) method was used to observe the oil concentration contour inside a slug using volume-of-fluid (VOF) with the species-transport model. Based on the simulation results, the oil concentration was accumulated in both the slug’s rear and front regions. Hence, the creation of four vortices resulted in the creation of dead zones at the low-oil-concentration region. Furthermore, it has been observed that an optimum flow rate in a microchannel reactor is required to achieve a high mass transfer. A higher oil concentration was measured during the slug formation at a low flow regime due to the long residence time. In contrast, a high mass transfer has been reported during the slug-moving stage due to the higher vortices velocity, resulting in enhanced mixing and mass transfer. Hence, slug forming and the moving stage substantially influenced mass transfer at low and high flow rates, respectively.