Objective: To explore the application value of physical rehabilitation programs in the treatment of patients with neck, shoulder, waist and leg pain. Methods: 80 patients were studied, all diagnosed with neck, shoulder, waist and leg pain after admission. After being divided into groups according to the odd-even number method, 40 cases were assigned to each group. The selection time of the two groups started in January 2025 and ended in December 2025. During the treatment phase, conventional Western medicine was used in the control group and a physical rehabilitation program was used in the experimental group. The final effect was evaluated and compared, including: VAS score (visual analogue scale for pain), clinical efficacy and quality of life in patients with neck, shoulder, waist and leg pain. Results: (1) After statistics of VAS scores of patients with neck, shoulder, waist and leg pain, the difference before treatment was small, P > 0.05; after treatment, both groups improved, and the experimental group (3.18 ± 0.47 points) was at a lower level, P < 0.05; (2) In terms of total effective rate, conventional Western medicine treatment, The statistical data of physical rehabilitation treatment were: 80.00% (32/40), 95.00% (38/40). The comparison results showed that the experimental group was higher, P < 0.05; (3) In the quality of life scores, the patients with neck, shoulder, waist and leg pain in the experimental group were higher, P < 0.05. Conclusion: In the clinical treatment stage, the physical rehabilitation program is effective. For patients with neck, shoulder, waist and leg pain, it can significantly improve pain symptoms and other disease symptoms, and promote an improvement in the total effectiveness. At the same time, this program can also better protect the best quality of life for patients, and has significant promotional value.