The Da Vinci robot-assisted surgical technology signifies a substantial advancement in pediatric surgery for the treatment of congenital structural malformations. This research endeavor aims to perform a comprehensive comparative analysis of the therapeutic efficacy and assess the clinical applicability and value of the Da Vinci robot-assisted surgical method in relation to the conventional laparoscopic surgical technique, particularly in the management of congenital choledochal cysts. A retrospective cohort study was conducted involving 117 pediatric patients diagnosed with congenital choledochal cysts, who were admitted to the Affiliated Hospital of Zunyi Medical University between January 2019 and October 2024. Patients were categorized into two groups based on the surgical approach: the robot-assisted surgery group (RS group, n = 45) and the traditional laparoscopic surgery group (LS group, n = 72). Basic demographic and clinical data, perioperative parameters-including operation duration and intraoperative blood loss-and postoperative complications were systematically collected and statistically analyzed for both groups. The operating time in the robotic surgery (RS) group was 224.5 (203.3, 247.7) minutes, significantly longer than the 190.2 (170.5, 219.7) minutes recorded in the laparoscopic surgery (LS) group, with a statistically significant difference (P < 0.05). No conversions to open surgery occurred in either group. Intraoperative blood loss in the RS group was 11.5 (9.4, 13.4) ml, which was significantly less than the 19.8 (14.7, 26.6) ml observed in the LS group (P < 0.001). The postoperative drainage tube retention time was 4.5 (4, 6) days in the RS group compared to 5.8 (4, 7) days in the LS group, with a statistically significant difference (z = -3.285, P = 0.001). The postoperative hospital stay averaged 9 (7, 11) days for the RS group, while the LS group had an average of 11 (10, 13) days, also showing a statistically significant difference (z = -4.520, P < 0.001). During the follow-up period, complications were reported in 1 case [2.22% (1/45)] in the RS group, whereas 6 cases [8.33% (6/72)] were reported in the LS group. However, there was no statistically significant difference in complication rates between the two groups (P = 0.424). Robot-assisted treatment of congenital choledochal cysts is considered both safe and reliable. This technique minimizes the complexity of hepaticojejunal anastomosis and decreases the duration of the anastomosis. Furthermore, it provides several advantages, including reduced intraoperative blood loss, a low rate of postoperative complications, and a faster recovery period.