Identification and localization of parathyroid glands (PGs) remains a challenge for surgeons. The aim of this study was to evaluate the efficiency of intraoperative near-infrared autofluorescence (NIRAF) imaging to detect PGs in thyroid and parathyroid diseases. Seventy-six patients undergoing surgery for thyroid or parathyroid diseases between July 9, 2020 and August 20, 2021 were retrospectively analyzed. Intraoperative carbon nanoparticle (CN) negative imaging and handheld NIRAF imaging were successively performed for each patient. Of 206 PGs that needed to be identified for surgery, 162 were identified by NIRAF imaging, with a theoretical rate of identification of 78.64%. This was higher than the rate of identification with CN negative imaging, which was 75.73%. The number of PGs identified by NIRAF imaging and CN negative imaging did not differ significantly in either total thyroidectomy or thyroid lobectomy. In addition, the autofluorescence (AF) intensity of secondary parathyroid adenoma was weaker than that of normal PGs. NIRAF imaging is potentially a more efficient tool for identification of PGs than CN negative imaging, with a shorter learning curve and lower risk. It may not be well-suited to secondary hyperthyroidism or adenoma, but it was more efficient at identifying excised specimens than visual identification by a surgeon.