To capture both epithelial and mesenchymal subpopulations of CTCs at different metastatic stages of PCa patients, here we constructed a novel dual-antibody-functionalized microfluidic device by employing antibodies against PSMA and EpCAM. In vitro experiments with the dual capture system for capturing both LnCAP and LnCAP-EMT cells have shown significantly enhanced capture efficiency as compared to that of the EpCAM single capture system. Furthermore, the dual capture system could successfully identify CTCs in 20 out of 24 (83.3%) PCa patients, and the CTCs counts from the dual capture system were statistically correlated with the TNM stage of patients ( P < 0.05), while conventional diagnostic methods, such as serum PSA level and Gleason score, failed to correlate to patient TNM stages. To further explore potential clinical application of our dual capture system, captured CTCs were recovered and subjected to qRT-PCR to quantify known factors involved in PCa development and therapy. The results demonstrated that the combined detection of SChLAP1 and PSA in CTCs is a potential marker for identifying patients with metastatic PCa, while detection of AR and PD-L1 in CTCs may have the potential to determine the sensitivity of PCa patients to androgen deprivation therapy and immunotherapy, respectively. Taken together, the dual-antibody-functionalized microfluidic device established in our study overcomes the limitations of some CTC capture platforms that only detect epithelial or mesenchymal CTCs in PCa patients, and detection of the PCa-related RNA signatures from purified CTCs holds great promise to offer warnings for early metastasis of PCa and may provide guidance for therapy decisions.