A novel microfluidic approach is developed to prepare multicolor QDs-encoded core-shell microparticles with precise and various barcode and enhanced stability performance. With the protection of the hydrogel shell, the leakage of QDs is avoided and the fluorescent stability is enhanced greatly. By embedding different QDs into different cores, no interaction between different QDs existed and the fluorescence spectrum of each kind of QDs can be recorded, respectively. Compared with QDs mixtures in a single particle, it is unnecessary to separate the emissions of QDs in different colors, and deconvolution algorithms are not needed. Therefore, it still maintains precise coding even if QDs with approximate emission wavelengths are used.