The rapid, precise, and automated diagnosis of infectious diseases is crucial for effective disease management and control. Herein, the integrated portable and automatic digital detection system (IPADS), a novel diagnostic platform for nucleic acid detection is introduced. The device employs the hybrid magnetic system (HMS), which uses an electromagnet and a movable permanent magnet to modulate the magnetic field and control bead movement, increasing nucleic acid extraction efficiency to over 80%, while simplifying the traditional labor‐intensive process and enabling quick, low‐risk sample processing. Additionally, a disposable cartridge is designed for integrated HMS based preprocessing, with detection performed using digital RPA‐Cas12a, enabling rapid, enclosed, and automation‐friendly detection across a dynamic range spanning five orders of magnitude, with a sensitivity as low as 100 copies mL−1 in serum samples. An automated platform further optimizes workflow. As a proof of concept, IPADS is applied to detect hepatitis B virus (HBV) DNA in 20 clinical serum samples, demonstrating high concordance with gold‐standard quantitative PCR (qPCR) methods. These results validate the potential of IPADS as a reliable point‐of‐care testing solution.