Experiments were carried out in a slug flow microreactor to systematically investigate reaction behavior under variation of flow rate, and a comparative study was made. Y-junction microreactor and T-junction microreactor have been used to extract yttrium(III) using 2-ethylhexyl phosphonic acid mono-2-ethylhexyl (EHEHPA or P507). Results show that the maximum extraction efficiency of 90.4% in both microreactors could be achieved corresponding to the minimum flow rate of 10 and 100 μL/min. The values of specific interfacial area remain unchanged with the increase of flow rate, and the specific interfacial area of the Y-junction serpentine microreactor is much higher than that of the T-junction microreactor. Maximum values of volumetric mass-transfer coefficient (1.642 s–1) in the Y-junction microreactor are found to be several orders of magnitude higher than those of the T-junction microchannel (0.043 s–1) and conventional extractors (0.0197 s–1).