The occurrence and development of diseases are closely related to overexpression of specific biomarkers in the serum of patients. Rapid and sensitive biomarker detection is beneficial for early diagnosis and treatment. However, the current laboratory processes and assays for biomarker detection are expensive and time-consuming, and their operation also requires a large number of professionals. We developed a magnetically modulated differential quartz crystal microbalance (MMD-QCM) method combined with magnetic bead (MB) labels for rapid and highly sensitive quantitative detection of prostate-specific antigen (PSA). Because MBs exhibit magnetized rotation motion under an applied AC magnetic field, a pair of QCMs are utilized to measure the difference between the magnetic motion intensities of the MBs and the MB−PSA immune complex to determine the PSA concentration. Experimental results demonstrate that the proposed method can be adopted to determine the PSA concentration in a wide range of 0.01− 1000 ng/mL as well as exhibit a low detection limit of 0.065 ng/mL. In addition, the proposed scheme enables fast detection and low sample consumption. The single detection process takes less than 4 h and requires only 113 μL of sample solution. The proposed detection strategy is superior to the existing detection method and can be effectively used in early screening and prognostic diagnosis of cancer and other related diseases owing to its simplicity, low cost, and high speed.