Objective To compare the efficacy and safety of endoscopic scissors plus ultrasonic scalpel and ultrasonic scalpel only to free flap during endoscopic thyroidectomy. Methods A total of 128 patients were randomly divided into two groups, including 60 cases using endoscopic scissors plus ultrasonic scalpel and 68 cases using ultrasonic scalpel only. The free flap time, gas consumption, blood loss, and subcutaneous drainage 48 h after surgery were recorded for both groups. Postoperative follow-up was conducted 1 month after the surgery to record patients' local skin paresthesia. Results All surgeries were performed well. No significant differences were found between the two groups in the amount of blood loss, subcutaneous drainage at 48 h, and local flap paresthesia after 1 month (P> 0.05). However, the free flap time and gas consumption were significantly different (P<0.05). Conclusion The reasonable application of endoscopic scissors plus ultrasonic scalpe can expand the operating space for endoscopic thyroidectomy rapidly, especially for the free flap of thoracic region. Meanwhile, it can reduce the amount of gas consumption and shorten the time of free flap, without increasing the amount of intraoperative blood loss and subcutaneous drainage 48 h after surgery. This method is safe and effective, thus it is worth popularizing.