Pulmonary dysfunction is very common in stroke patients. A study has shown that acute stroke patients often cause a series of pulmonary dysfunction due to primary damage to the respiratory center, which is an important reason for hindering disease treatment and recovery. American Thoracic Society (ATS) and the European Respiratory Society (ERS) pointed out that pulmonary rehabilitation (PR) can be applied to the rehabilitation of stroke patients to improve their lung function. PR can improve the respiratory muscle strength of stroke patients, which is beneficial to improving the respiratory function of patients. At the same time, it can also significantly increase the maximum oxygen intake of patients, effectively improve the cardiopulmonary function of stroke patients, and reduce respiratory complications such as aspiration pneumonia. However, the common dysfunction of joints and muscles such as shoulder pain after stroke will affect the process of pulmonary rehabilitation. This is mainly because the changes in the position of the shoulder girdle, the decrease in the range of motion of the cervical and thoracic spine, and the changes in the cervical spondylolisthesis position caused by the elevation of the upper limbs will directly affect the breathing movement during the pulmonary rehabilitation process. The instability of the spine will weaken the deep abdominal muscles and reduce the function of the diaphragm; moreover, changes in the alignment and stability of the cervical and thoracic spine will also lead to wrong breathing methods. Therefore, it is of practical clinical significance to evaluate the functional rehabilitation of shoulder joint muscles and evaluate the efficacy of stroke patients to improve their respiratory function. This article through an extensive review of domestic and foreign literature in recent years, combined with clinical practice experience, summarizes the practical application of chain structure theory in the fields of rehabilitation training, postural adjustment, pain relief, etc., and further studies the functional exercise method based on muscle chain theory. The research on the muscle chain of shoulder pain rehabilitation as a model illustrates the positive effect of reconstructing neuroarticular muscle function on the respiratory system, hoping to provide new ideas for the treatment of respiratory diseases in stroke patients.