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Stimulated emission depletion microscopy (STED) holds great potential in biological science applications, especially in studying nanoscale subcellular structures. However, multi-color STED imaging in live-cell remains challenging due to the limited excitation wavelengths and large amount of laser radiation. Here, we develop a multiplexed live-cell STED method to observe more structures simultaneously with limited photo-bleaching and photo-cytotoxicity. By separating live-cell fluorescent probes with similar spectral properties using phasor analysis, our method enables five-color live-cell STED imaging and reveals long-term interactions between different subcellular structures. The results here provide an avenue for understanding the complex and delicate interactome of subcellular structures in live-cell.