Objective To summarize the clinical data of 3 children with autoimmune polyendocrinopathy syndrome (APS) with renal impairment, so as to improve the understanding of the disease. Methods The clinical and renal biopsy pathological data of 3 children with APS complicated with renal damage hospitalized in the Kidney Department of Children's Hospital Affiliated to Nanjing Medical University from February 2018 to February 2023 were retrospectively analyzed. Results Among the 3 patients, 2 were girls and 1 was a boy. The onset age ranged from 1 year and 4 months to 9 years and 11 months. All children with endocrine gland damage presented with autoimmune thyroid disease with type 1 diabetes and were diagnosed with APS type 3. The clinical manifestation of 1 patient was acute renal failure, renal tubular acidosis typeⅠ, and pathological manifestation was tubulointerstitial nephritis. One patient showed hemolytic uremic syndrome, and the renal pathology manifested as thrombotic microangiopathy. One patient had mild tubular proteinuria clinically, and the pathology showed focal tubulointerstitial nephritis. No definite pathogenic gene variation was found in 3 patients. Two patients received oral rapamycin and 1 received a 1-dose infusion of rituximab. After a follow-up from 1 year to 2 years and 7 months, all patients showed normal urinalysis and normal renal function. Conclusions APS type 3 can be associated with renal damage, and its clinical manifestations and renal biopsy pathology are diversified.