Counter-current operation has been widely applied to enhance the extraction efficiency for systems with low distribution coefficients, which was hindered in microextraction because viscous force and surface tension dominate over gravity and inertial force. In this study, a novel design of a tube-in-tube microextractor relying on a poly tetra fluoroethylene membrane to construct a stable interface was proposed to conduct continuous counter-current extraction. Extraction kinetics for two systems with different distribution coefficients, membranes with different pore radii, and three flow rate ratios were measured as a function of residence time. For the system that toluene was used to extract 0.06 wt % phenol in water, 4.1 stages of extraction efficiency were achieved at a residence time of 9.8 min. A challenging case study (50 wt % acetone−water−toluene) was subsequently conducted to prove the high applicability for emulsion systems of this special microextractor. Lastly, a mathematical model was established and the predicted results of three flow rate ratios are in good agreement with experimental results.