Various types of botulinum toxin (BoNT) have been studied to treat cervical dystonia (CD). Although high-dose BoNT has proven efficacy, it increases the risk of adverse events. For this reason, this study was planned to identify the non-inferiority efficacy, tolerability, and safety of low-dose neubotulinum toxin A (Neu-BoNT-A) versus low-dose abobotulinum toxin A (Abo-BoNT-A) in CD treatment. The 48-week, prospective, randomized, controlled crossover design study of CD treatment, with 50-unit Neu-BoNT-A and 250-unit Abo-BoNT-A injections at 12-week intervals, was conducted over a 24-week treatment period. This study used the following standardized rating scales to assess the efficacy of BoNT: the Toronto Western Spasmodic Torticollis Rating Scale (TWSTRS); health-related quality of life (HRQoL); the Cervical Dystonia Impact Profile (CDIP-58); the Short Form 36 health survey questionnaire (SF-36); and, for the depressive symptoms of CD patients, the Center for Epidemiological Studies-Depression Scale (CES-D) and the Patient Health Questionnaire-9 (PHQ-9). Fifty-two CD patients were enrolled from October 2019 to January 2021. The mean scores of the TWSTRS total at the post-treatments in both Neu-BoNT-A and Abo-BoNT-A had a significant reduction from baseline (p = 0.008 and 0.002, respectively). However, the mean changes of the TWSTRS total at the 12- and 24-week treatments between the two treatment groups were not significantly different (p = 0.284 and 0.129, respectively). The mean scores of the HRQoL questionnaires (the CIDP-58 and the SF-36) and the depressive symptoms (the CES-D and the PHQ-9) in both treated groups at the post-treatments did not significantly decrease from baseline and were comparable. Two patients treated with Abo-BoNT-A (250 units) reported cervical tension and benign paroxysmal positional vertigo (BPPV). There were no serious adverse events reported. Though both low-dose BoNT-As were effective at improving clinical symptoms without significant side effects, both treatments did not predict change in quality of life and depression. With the non-inferiority criteria, low-dose Neu-BoNT-A has a similar efficacy, safety, and tolerability to Abo-BoNT-A.