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With the aim of efficiently sorting rare circulating tumor cells (CTCs) from blood and minimizing damage to CTCs during isolation, we constructed an inertia-assisted single-cell focusing generator (I-SCF) and a water droplet deterministic lateral displacement cell sorting (D-DLD) microfluidic system (IDIC) based on different sizes, the device is initially sorted by a continuous fluid swing and Dean flow-assisted helical micromixers, then flows through a droplet shaped DLD region, enabling single-cell focused sequencing and precise separation, improving cell separation efficiency (>95%) and purity, while ensuring a high single cells survival rate of more than 98.6%. Subsequently, breast cancer cell lines were run through our chip, and then the downstream epithelial-mesenchymal transition (EMT) process induced by TGF-β was detected, and the levels of three proteins, EpCAM, PD-L1, and N-cadherin, were analyzed to establish the relationship between PD-L1 and the EMT process. Compared with other analytical techniques such as the filtration method, the enrichment method and immunoaffinity capture methods, this method not only ensures the separation efficiency and purity, but also ensures the cell activity, and avoids missing the different results caused by the heterogeneity of CTCs due to the isolation of high purity (84.01%). The device has a high throughput processing capacity (5 mL of diluted whole blood/∼2.8 h). By using the chip, we can more easily and conveniently predict tumor stage and carry out cancer prevention and treatment in advance, and it is expected to be further developed into a clinical liquid biopsy technology in the future.