Point-of-care technology (POCT) has been widely applied for clinical detection and on-site test, playing an important role in rapid and portable molecular diagnosis. In this study, a novel microfluidic chip based real-time PCR device combined with dual temperature control modules (CQ100 system) has been developed for rapid clinical POCT test and gene diagnostics. The microfluidic chip has been automatically driven to repeatedly switch between two control modules with different temperatures (95℃ and 60℃). Two fluorescent channels were set to detect FAM and Cy5 fluorescence when the microfluidic chip stayed between two modules in each reaction cycle. Based on the CQ100 system, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was detected through two gene targets including ORF1ab and N genes. To evaluate the performance of this assay in comparison to the DA0990 assay approved by China FDA which is run on the ABI 7500 instrument, 500 clinical sputum specimens were collected from a local hospital and a local CDC lab during Feb to May in 2020 in this study. The results showed that it cost about 19min to finish both reverse transcriptional reaction and 40 cycles of PCR amplification, and the CQ100 system possessed an analytical sensitivity limit of 200 copies/mL for detection of SARS-CoV2, with no cross-reactions to other pathogens. A total of 12 SARS-CoV-2 positive samples (2.4%, 12/500) were detected by the assay run in the CQ100, which was the same as the results obtained by the DA0990 assay. Moreover, the CQ100 system turnaround time (19 min, not including RNA extraction) and cost (about 5.0 AU$) per specimen were less than those for the DA0990 assay (60 min, 17.15 AU$). In summary, this study provides a novel and portable microfluidic chip based real-time PCR instrument combined with a dual temperature control module for clinical molecular diagnosis. A rapid, accurate, easy-to use, and cost-effective diagnostic test for SARS-CoV-2 has been developed on the basis of the CQ100 system.