This prospective randomized controlled trial investigated the clinical value of sigmoid colon water exchange (SWE) colonoscopy by comparing it with air insufflation (AI) colonoscopy in terms of the patient’s pain score, insertion time, and screening quality. Consecutive patients who underwent colonoscopy without sedation were randomized into an AI group (n = 267) or an SWE group (n = 255). Patient characteristics, history of abdominal or pelvic surgery, maximum pain score, insertion time, cecal intubation rate, polyp detection rate, and the need for maneuvers were recorded. There was no significant between-group difference in insertion time, cecal intubation rate, assisted maneuvers (abdominal pressure, changing patients’ position), or polyp detection rate (P > 0.05). The mean maximum pain score was significantly lower in the SWE group than in the AI group. (3.57 ± 2.01 vs. 4.69 ± 1.83, P < 0.001). For patients with a history of abdominal or pelvic surgery and those who were overweight (body mass index > 24), the maximum pain scores were lower in the SWE group than in the AI group (3.67 ± 1.95 vs. 4.88 ± 1.80, P < 0.001; 3.40 ± 1.96 vs. 4.79 ± 1.97, P < 0.001, respectively). SWE colonoscopy can significantly reduce abdominal pain with non-inferior screening quality and does not increase insertion time.Trial registration number: ChiCTR2200059057 (date April 23, 2022).