Propofol sedation, routinely used for endoscopic procedures, is safe and acceptable for children. Adjuvants, such as esketamine or sufentanil, are commonly added to improve the efficacy and safety of propofol sedation. This study aimed to compare the clinical efficacy and safety of propofol-esketamine (PE) versus propofol-sufentanil (PS) for deep sedation and analgesia in children with autism undergoing colonoscopy procedure. One hundred and twenty-four children with autism undergoing colonoscopy procedure were included in the study. Patients were randomly assigned to receive one of the two adjuvants: esketamine (0.3 mg/kg) or sufentanil (0.2 μg/kg), subsequently administered propofol 2.0 mg/kg to induce anesthesia. Additional doses of propofol (0.5-1.0 mg/kg) were administered as needed to ensure patient tolerance for the remaining duration of the procedure. Movement during the procedure, hemodynamic variables, the total dose of propofol, recovery time, and adverse events were recorded. The PE group exhibited a significantly lower incidence of severe movement during the procedure compared with the PS group (14.52% vs. 32.26%, p = 0.020). The PE group showed significantly lower incidence of respiratory depression, hypotension, and severe injection pain of propofol than the PS group during the procedure (all p < 0.05). The mean arterial pressure (MAP) decreased significantly after anesthesia induction in the PS group and remained lower than baseline (all p < 0.05). Compared with the combination of low-dose sufentanil (0.2 μg/mg) with propofol, the low-dose esketamine (0.3 mg/kg) combined with propofol provided more stable hemodynamics, higher quality of sedation, and fewer adverse events in children with autism undergoing colonoscopy procedure.