To investigate the short-term effects and differences between exercise alone and exercise combined with self-mobilization training on chronic non-specific neck pain (CNSNP). Thirty subjects who met the criteria were recruited and randomly assigned to the exercise training group, the exercise combined with cervical self-mobilization training group (ECCM), and the exercise combined with cervicothoracic self-mobilization training group (ECCTM). The exercise training group received 6 weeks of deep neck flexor under biofeedback and scapular stability training, and the other two groups received 6 weeks of cervical self-mobilization and cervicothoracic self-mobilization, respectively, in addition to exercise training. Neck pain, cervical range of motion (ROM), neck disability, strength and endurance of deep neck flexor and quality of life were assessed before and after 6 weeks of training. The study results showed that all the three training programs for 6 weeks increased the strength and endurance of deep neck flexor, increased cervical ROM, reduced pain, and improved neck function (P < 0.05). The exercise combined with self-mobilization two groups compared with only the exercise training group had better improvement in ROM of extension, lateral flexion, rotation and quality of life (P < 0.05). Compared with exercise alone and exercise combined with cervical self-mobilization training, the exercise combined with cervicothoracic self-mobilization training was the best in improving ROM of right lateral flexion (exercise training group vs ECCTM: P < 0.01, d = 1.61, ECCM vs ECCTM: P < 0.05, d = 1.14) and pain (exercise training group vs ECCTM: P < 0.05, d = 1.34, ECCM vs ECCTM: P < 0.05, d = 1.23). Deep flexor muscle and shoulder stability training can improve the endurance and strength of the deep flexor muscles of the neck and coordinate the movement patterns of the shoulder and neck. Self-mobilization techniques can promote improvements in cervical lateral flexion and rotation range of motion, alleviate neck disability and further improve quality of life. A combination of exercise and cervicothoracic self-mobilization training appears beneficial for the management of neck pain.