The current randomized controlled trial was performed at the China Rehabilitation Science Institute, China to test the hypothesis that musical auditory stimulation has positive effects on the autonomic nervous system of patients with disorder of consciousness. Although past studies have recommended that patients with disorder of consciousness listen to patient-preferred music, this practice is not universally accepted by researchers. Twenty patients with severe disorder of consciousness listened to either therapist-selected (n = 10, 6 males and 4 females; 43.33 ± 18.76 years old) or patient-preferred (n = 10, 5 males and 5 females, 48.83 ± 18.79 years old) musical therapy, 30 minutes/day, 5 times/week for 6 weeks. The results showed no obvious differences in heart rate variability-related parameters including heart rate, standard deviation of normal-to-normal R-R intervals, and the root-mean-square of successive heartbeat interval differences of successive heartbeat intervals between the two groups of patients. However, percentage of differences exceeding 50 ms between adjacent normal number of intervals, low-frequency power/high-frequency power, high-frequency power norm, low-frequency power norm, and total power were higher in patients receiving therapist-selected music than in patients receiving their own preferred music. In contrast, this relationship was reversed for the high-frequency power and very-low-frequency band. These results suggest that compared with preferred musical stimulation, therapist-selected musical stimulation resulted in higher interactive activity of the autonomic nervous system. Therefore, therapist-selected musical stimulation should be used to arouse the autonomic nervous system of patients with disorder of consciousness. This study was approved by the Institutional Ethics Committee of China Rehabilitation Research Center, China (approval No. 2018-022-1) on March 12, 2018 and registered with the Chinese Clinical Trial Registry (registration number ChiCTR1800017809) on August 15, 2018.