Background: Surgical extraction of the third molar is the most common surgical procedure in the oral surgery field and is associated with several complications. This study aimed to compare the effects of a newly presented suturing technique with the routine suture after surgical removal of the third molar on the postoperative complications. Materials and methods: This randomized clinical trial was designed as a split-mouth double-blinded investigation. Twenty patients were involved in the current study. After the surgical removal of the third molar, the new suturing technique was used to close the wound on one side of the patient randomly (case side), and the other side was sutured by the routine simple interrupted stitches (control side). Pain, edema, trismus, pocket depth, and the attachment loss of the distal of the second molar were assessed following the surgery. The data were statistically analyzed and compared between the sides. Results: Pain and edema following the surgery in the control side were significantly less than in the case side. The pocket depth and the gingival attachment loss of the distal aspect of the second molar in the case side were significantly less than in the control side. No case of dry socket was observed in the case side. Conclusion It seems that the newly presented suturing technique is able to keep the wound margins close to each other and may be helpful in reducing the periodontal complication of the second molar following the surgical removal of the impacted third molars.