Three-dimensional high-definition manometry was used in evaluating anorectal function of 142 post-operative patients with anorectal malformations (ARMs), while 104 non-operative children as controls (CON) who were subdivided into different age groups. Data were collected on the functional length (HPZ-length), resting and squeeze pressure (HPZ-rest, HPZ-sqze), recto-anal inhibitory reflex (RAIR), and strength distribution of the anal canal. The results showed a gradual increase in anal canal function parameters with age in normal infants and children, suggesting that age should be considered as an essential factor when evaluating post-operative anorectal function in ARMs patients. Comparing with CON, a significant decrease in HPZ-rest was observed in all post-operative ARMs groups (p < 0.05). The majority of ARMs patients with incontinence had significantly lower HPZ-rest and a higher percentage of asymmetric strength distribution compared to those with continence (p < 0.05). The type classification of high and cloaca in ARMs, as well as low HPZ-rest, were identified as two factors affecting post-operative functional outcomes. Manometry is a valuable modality providing distinct details of anal function in the assessment of the underlying functional causes of postoperative defecation disorder, thus helping physicians select the right modality of treatment. Sequential manometry studies are useful for re-evaluating anal function after treatment and biofeedback training.