Liquid⁻liquid two-phase flow in microchannels has attracted much attention, due to the superiority of mass transfer enhancement. One of the biggest unresolved challenges is the low mixing efficiency at the microscale. Suitable mixing efficiency is important to promote the mass transfer of two-phase flow in microchannels. In this paper, the mixing efficiency in three junction configurations, including a cross-shaped junction, a cross-shaped T-junction, and a T-junction, is investigated by the volume of fluid (VOF) method coupled with user-defined scalar (UDS) model. All three junction configurations are designed with the same hydraulic diameter of 100 μm. Mixing components are distributed in the front and back parts of the droplet. The mixing efficiency in the droplet forming stage and the droplet moving stage are compared quantitatively. Results show that different junction configurations create very different mixing efficiencies, and the cross-shaped T-junction performs best, with relatively lower disperse phase fractions. However, with an increase of the disperse phase fraction, the cross-shaped junction is superior.