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Traditional techniques involve embedding cells in crosslinked polymers to create continuous microgels, suitable mainly for adherent cells, or encapsulating them in droplets for only short\u2010term analysis, due to their instability. In this study, we developed a method for encapsulating single cells in liquid\u2010core microcapsules to address these limitations. The liquid encapsulation system is generated in an all aqueous environment through polymeric electrostatic interactions. Additionally, we design an innovative and low cost sorting system utilizing magnetic nanoparticles (MNPs) to efficiently select single\u2010cell encapsulated units for further analysis and applications. This system is tested with both suspension and adherent cell types, demonstrating cytocompatibility and no abnormal effects on cell behavior. The MNP\u2010based sorting achieved nearly 80% purity of the single\u2010cell population. 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