Background: This article presents a clinical application for a comprehensive and systematic auricular diagnosis protocol for musculoskeletal system disorder and a treatment protocol for chronic low-back pain (CLBP). This protocol includes (1) locating the somatotopic correspondences between the auricular zone and musculoskeletal system, (2) visual inspection, (3) palpitation, and (4) electrical detection. Methodology: To treat CLBP, the current authors have developed an auricular therapy protocol. In this CLBP protocol, the selection of ear acupuncture points (EAPs) takes into account (1) corresponding points, (2) points featuring both disharmony of Zang organs and disturbance of meridians, and (3) active points located at the Waist triangle, groove of Spinal posterior, and groove of Sciatic posterior areas of the ear. The Chinese Standard Ear-Acupoints Chart is used to locate the EAPs. The clinical application of this comprehensive and systematic auricular diagnosis protocol for diagnosing musculoskeletal system disorder is summarized. A treatment protocol for CLBP is presented that can be replicated by clinicians or researchers for pain managment. Conclusions: Auricular therapy is a relatively safe treatment, having minimal adverse effects in patients who have chronic pain. The treatment can be used as an adjunct therapy with conventional biomedical treatments.