Objective To explore the effect of deep muscle stimulation (DMS) combined with exercise therapy on morphological changes of the trapezius muscle assessed by musculoskeletal ultrasound and the function for patients with neck and shoulder myofascial pain syndrome (MPS). Methods One hundred and twenty patients with neck and shoulder MPS admitted to the First People’s Hospital of Shuangliu District, Chengdu between August 2021 and December 2022 were randomly selected and divided into 4 groups. There were 30 cases in each group. Group A received modulated middle frequency electrotherapy, group B received modulated middle frequency electrotherapy combined with DMS, group C received modulated middle frequency electrotherapy combined with exercise therapy, and group D received modulated middle frequency electrotherapy, DMS combined with exercise therapy. Before treatment and after 4 weeks of treatment, shear wave elastography was used to detect the shear wave velocity (SWV) of the four groups, high frequency ultrasound was used to detect the muscle thickness of the trapezius muscle. The Visual Analogue Scale (VAS) scores, Neck Disability Index (NDI), modified Barthel Index (MBI), Instrumental Activities of Daily Living Scale (IADL), World Health Organization Quality of Life-BREF (WHOQOL-BREF), Self-rating Anxiety Scale (SAS), and Self-rating Anxiety Scale (SDS) were also assessed to compare the therapeutic effects among the four groups of patients under different intervention methods. Results Before treatment, there was no significant difference in trapezius muscle SWV, trapezius muscle thickness, VAS, NDI, MBI, IADL, WHOQOL-BREF, SAS or SDS among the four groups (P>0.05). After 4 weeks of treatment, there were significant differences in trapezius muscle SWV, VAS, NDI, WHOQOL-BREF in the physiological domain and psychological domain, SAS and SDS among the four groups (P<0.05), and the improvements of trapezius muscle SWV, WHOQOL-BREF in the physiological domain and psychological domain, and SDS in group D were more obvious than those in other groups (P<0.05). After 4 weeks of treatment, there was no significant difference in MBI, IADL, or WHOQOL-BREF in the society domain and environmental domain among the four groups (P>0.05). Conclusion DMS combined with exercise therapy can significantly improve trapezius muscle elasticity, psychological state and quality of life of patients with neck and shoulder MPS.