Objective To explore the relationship between spinal cord dysplasia and congenital complex anorectal malformations (ARMs) and how they affect the defecatory function in children. Methods We retrospectively analyzed the clinical data of 148 children undergoing staged surgeries for complex ARMs between October, 2012 and February, 2017. According to the findings by lumbosacral magnetic resonance imaging (MRI), the children were divided into normal spinal cord group and abnormal spinal cord development group to analyze the distribution of spinal cord dysplasia in different types of ARMs and the impact of anomalies in spinal cord development on the development of the perianal muscles, anorectal manometry, and the defecatory function. Results Of the 148 children, 34 (23.0%) showed anomalies in spinal cord development, including steatosis of the terminal filament in 21 (61.8%) cases, intraspinal lipoma in 7 (20.6%) cases, syringomyelia in 1 (2.9%) case, intraspinal cystic lesion in 3 (8.8%) cases, and mixed spinal cord anomaly in 2 (5.9%) cases. We classified AMRs into different types according to Krickenbeck international classification, and abnormal spinal cord development was found in 20.0% (1/5) of the patients with rectal stenosis, 25.0% (5/20) of the patients with rectal atresia, 20.0% (1/5) of the patients with perineal fistula, 22.2% (8/36) of the patients with rectobulbar fistula, 18.2% (6/33) of the patients with rectoprostatic fistula, 25.0% (1/4) of the patients with rectovesical fistula, 24.2% (8/33) of the patients with vestibular fistula, 66.7%(2/3) of the patients with rectovaginal fistula, and 22.2% (2/9) of the patients with cloaca; No significant difference was found in the incidences of abnormal spinal cord development among the 9 groups (P=0.874). A total of 145 patients were evaluated for perianal muscle development during the surgery, and 26 patients had excellent, 105 had good, and 14 had poor development; the development of perianal muscles differed significantly between the children with normal and those with abnormal spinal cord development (P=0.005). Forty-four patients received anorectal manometry, which Showing no significant difference in resting anal pressure between the children with normal and abnormal spinal cord development (35.0±14.8 vs 27.9±14.3 mmHg, P=0.268); the positivity rate of rectoanal inhibitory reflex (RAIR) was lower in normal spinal cord group than in spinal cord dysplasia group (45.9% vs 71.4%), but the difference was not statistically significant (P=0.412). Follow-up of the patients for defecatory function assessment using the modified Rintal scale showed no significant difference in the constituent ratios of defecatory function between the 2 groups (P=0.416). Conclusion Spinal cord dysplasia is associated with perianal muscle development in children with complex ARMs, for whom routine lumbosacral MRI should be performed to detect the presence of spinal cord dysplasia.