In this paper, we have compared and analyzed the effect of laparoscopic and open surgical treatments in children with congenital megacolon. To address this, a total of 64 children with congenital megacolon who underwent surgery in the hospital, particularly from April 2014 to December 2020, were selected as the research objects. They were divided into control and observation groups by the random number table method, with 32 cases in each group. The control and observation groups were treated with open surgical and laparoscopic treatments, respectively. The treatment effects of the two groups were compared. The enema time, operation time, blood loss, anal defecation time, and duration of postoperative hospital stay of the observation group were lower than those of the control group. The comparison between the two groups was statistically significant (P < 0.05). There was no significant difference in CRP and WBC between the two groups before surgery (P > 0.05). The CRP level and WBC of the two groups were both increased after operation, the CRP level of the observation group was lower than that of the control group, the difference was statistically significant (P < 0.05), the WBC of the two groups was not statistically significant (P > 0.05). The rate of excellent and good defecation in the observation group on the 7th day after surgery was higher than that in the control group, and the difference was statistically significant (P < 0.05). There was no significant difference in Krickenbeck scores between the two groups before surgery (P > 0.05); 6 months after the surgery, the score of Krickenbeck in both groups increased, and that of the observation group was higher than that of the control group, indicating a difference in the overall score (P < 0.05). The total complication rate within 7 days after surgery in the observation group was lower than that in the control group, and the difference was not statistically significant (P > 0.05). Laparoscopic treatment of congenital megacolon could improve surgical indicators and reduce stress response in children, improve defecation and anal function, reduce the risk of complications, and promote recovery.