While advances in microfluidics have enabled rapid and highly integrated detection of nucleic acid targets, the detection sensitivity is still unsatisfactory in the current POC (point-of-care) detection systems, especially for low abundance samples. In this study, a chip that integrates rapid nucleic acid extraction based on IFAST (immiscible phase filtration assisted by surface tension) and digital isothermal detection was developed to achieve highly sensitive POC detection within 60 min. Based on the interface theory, the factors influencing the interface stability of the IFAST process were studied, and the IFAST nucleic acid extraction conditions were optimized to increase the nucleic acid extraction recovery rate to 75%. Spiral mixing channel and flow-focusing droplet generation structure were designed to achieve the mixing and sample partitioning by applying negative pressure. A portable microdroplet fluorescence detection device was developed based on smartphone imaging. Validation tests were carried out for quantification of low-abundance cfDNA and detection of mutations.