For the analysis of biological analytes in complex matrices, it is difficult to achieve extraction of analytes and enrichment in an aqueous-aqueous single-drop microextraction system. In this study, we proposed a pH-dependent polydopamine (PDA)-coated vesicle/Fe3O4 magnetic aqueous-aqueous in a single-drop microreactor (SDMR) for the direct fluorescence detection of glutathione S-transferase (GST), a metabolic enzyme involved with crucial biological processes, in biological samples. After extracting and enriching the GST target from an aqueous-aqueous single-drop interface, the extraction process was conducted rapidly in 6 s in the SDMR system. The GST was first extracted from the sample solution via the GST-Aptamer on the polydopamine-coated vesicle/Fe3O4 nanospheres (Fe3O4@PDA@GST-Aptamer). Then, as the pH changed from weakly acidic to weakly alkaline in the SDMR system, the GST and GST-Aptamer were released from Fe3O4@PDA@GST-Aptamer nanospheres and captured by polydiacetylene vesicles via the capture probe. These changes altered the effective conjugation length and angle of the vesicle trunk, generating a highly enhanced fluorescence signal. This not only achieved the purpose of target enrichment but also reduced interferences posed by matrix effects. The approach can be used for the direct detection of GST in genuine urine and blood without any sample pretreatment. The linear range was 0.005 to 0.5 μg/mL, and the limit of detection was 0.834 ng/mL. The recoveries of GST in genuine blood samples ranged from 90.8 to 108.0% and in urine from 91.6 to 102.8%. The method has the capability of handling complex samples directly by enabling microextraction in an aqueous-aqueous single-drop system.