Iatrogenic unilateral vocal fold paralysis caused by thyroid surgery induces profound physical and psychosocial distress in patients. The natural course of functional recovery over time differs substantially across subjects, but the mechanisms underlying this difference remain unclear. In this study, we examined whether the anatomic site of the lesion affected the trajectory of recovery. In this prospective case series study in a single medical center, patients with thyroid surgery-related unilateral vocal fold paralysis were evaluated using quantitative laryngeal electromyography, videolaryngostroboscopy, voice acoustic analysis, the Voice Outcome Survey, and the Short Form-36 quality-of-life questionnaire. Patients with and without superior laryngeal nerve injuries were compared. Forty-two patients were recruited, among whom 15 and 27 were assigned to the with and without superior laryngeal nerve injury groups, respectively. Compared with the group without superior laryngeal nerve injury, the group with superior laryngeal nerve injury group demonstrated less improvement in the recruitment of vocal fold adductors, and the group also had more severe impairment of vocal fold vibration, maximum phonation time, jitter, shimmer, and harmony-to-noise ratio at the first evaluation. This difference was also found in the glottal gap and maximum phonation time 12 months after the injury. Among patients with thyroid surgery-related unilateral vocal fold paralysis, superior laryngeal nerve injury induces a distinctively different recovery trajectory compared with those without superior laryngeal nerve injury characterized by less reinnervation of vocal fold adductors and worse presentation in terms of the glottal gap and maximum phonation time. This study emphasizes the importance of superior laryngeal nerve function and its preservation in thyroid surgery.