The augmented reality-assisted navigation system (AR-ANS) has been initially applied to the management of hepatolithiasis. The current study examines the safety and efficacy of the AR-ANS for hepatectomy in the treatment of hepatolithiasis. It is the first study to assess the preoperative and long-term outcomes of hepatectomy guided by the AR-ANS for hepatolithiasis.From January 2018 to December 2021, 77 patients with hepatolithiasis who underwent hepatectomy at Zhujiang Hospital of Southern Medical University were included. The subjects were divided into the AR group (n = 31) and the non-AR group (n = 46) according to whether the surgery was guided by the AR-ANS. Clinical baseline features, operation time, intraoperative blood loss, immediate postoperative residual stone rate, postoperative stone recurrence rate at 6 months, and postoperative complications were analyzed.There was no significant difference between preoperative baseline data from the 2 groups (p > 0.05). The AR group had a longer surgical time than the non-AR group (p < 0.001). The intraoperative blood loss in the AR group was lower than in the non-AR group (p < 0.001). Alanine transaminase, aminotransferase, immediate residual stone rate, and stone recurrence rate in the AR group were lower than in the non-AR group (p < 0.05). There was no significant difference in postoperative complications between the 2 groups.The application of the AR-ANS in hepatectomy for hepatolithiasis has not only achieved satisfactory therapeutic efficacy, but has also shown significant advantages in reducing intraoperative blood loss, immediate stone residual rate, and stone recurrence rate, which has clinical promotion value.