Pharyngeal swab nucleic acid detection plays an important role in the diagnosis of viral infectious diseases. This article proposes a novel nucleic acid sampling method by designing a digital flexible manipulator (DFM) that capable of sensing the force at its tip. Force sensing contributes to achieving quantitative sampling, reducing the design complexity of the automated sampling robot’s visual system, and protecting the sampled area from harm. A mathematical model for evaluating the relationship between the force exerted on the tip of the manipulator and the voltage output of the Hall sensor was established, and based on this model, a prototype of the proposed DFM consisting mainly of Hall sensor, spring, permanent magnet, microcontroller, digital tube, and buzzer was fabricated. A series of experiments, including gentle contacting between the tip of the DFM and the surface, contacting force testing, and simulation of nucleic acid sampling, was performed to validate the proposed method. The experimental results revealed that the theoretically predicted force at the tip of the manipulator deviates from the actual force by a range of less than 7.4%, with a standard deviation smaller than 0.16 N. The DFM proposed in this article can assist the nucleic acid sampling medical staff in accurate sampling and provides a basis for designing a nucleic acid robotic arm with fully automated sampling capabilities.