Microalgae are renewable, sustainable, and economical sources of biofuels and are capable of addressing pressing global demand for energy security. However, two challenging issues to produce high-level biofuels are to separate promising algal strains and protect biofuels from contamination of undesired bacteria, which rely on an economical and high-resolution separation technology. Separation technology based on induced-charge electroosmotic (ICEO) vortices offers excellent promise in economical microalga separation for producing biofuels because of its reconfigurable and flexible profiles and sensitive and precise selectivity. In this work, a practical ICEO vortex device is developed to facilitate high-resolution isolation of rich-lipid microalgae for the first time. We investigate electrokinetic equilibrium states of particles and particle-fluid ICEO effect in binary-particle manipulation. Nanoparticle separation is performed to demonstrate the feasibility and resolution of this device, yielding clear separation. Afterward, we leverage this technology in isolation of Chlorella vulgaris from heterogeneous microalgae with the purity exceeding 96.4%. Besides, this platform is successfully engineered for the extraction of single-cell Oocystis sp., obtaining the purity surpassing 95.2%. Moreover, with modulating parameters, we isolate desired-cell-number Oocystis sp. enabling us to investigate proliferation mode and carry out transcriptome analyses of Oocystis sp. for high-quality neutral lipids. This platform can be extended directly to economically separate other biological micro/nanosamples to address pressing issues, involving energy security, environmental monitoring, and disease diagnosis.