Background Temporomandibular joint disorder (TMD) affects millions of people. It is unclear if low intensity ultrasound (US) is effective to treat TMD. Methods A total of 160 patients with TMD were enrolled in this study. The subjects were randomized into two groups to receive US therapy or no therapy. Patients in the US group were given US therapy once a day for 5 days per week for 2 consecutive weeks. Before and 4 weeks and 6 months after the treatments, the patients were assessed for pain using visual analog scale (VAS) and the maximum pain-free inter-incisal distance (IID). In addition, mandibular movement (MM), jaw noise (JN), disability index (DI) and craniomandibular index (CMI) were also assessed. Results Compared with the patients before the therapy, VAS, IID, MM, JN, DI and CMI in the US group were significantly improved 4 weeks and 6 months after therapy. However, 6 months after the therapy, US group had a recurrence rate of 2.63%. Conclusion US therapy can significantly reduce the pain, and improve the functionality of the temporomandibular joint and mouth opening limit for TMD patients, and is therefore recommended for TMD patients.