Objective To explore the influencing factors of the image cleanliness scores of magnetically-controlled capsule endoscopy (MCE) and the methods to improve cleanliness scores. Methods Data of patients undergoing MCE from October 2017 to August 2020 in Peking University First Hospital were analyzed retrospectively. The cleanliness scores at six regions of the stomach (cardia, fundus, body, angularis, antrum, and pylorus) were recorded (1-4 points), and the sum of the scores from these six regions was also calculated. Clinical features [gender, age, body mass index, indication, use of esophagus cap, and medication of proton pump inhibitors(PPI)], and gastric preparation regimens (one dose of pronase: simethicone 5 mL + pronase 20 000 U + sodium bicarbonate 1 g; or two doses of pronase: simethicone 5 mL + pronase 40 000 U + sodium bicarbonate 2 g) were collected. Cleanliness scores were defined as poor (group P, total cleanliness scores≤18) and as good (group G, total cleanliness scores>18). Clinical features, indication, use of esophagus cap and PPI, and preparation regimes were compared. Factors influencing cleanliness scores were analyzed. Results A total of 238 consecutive patients with median age of 61.5 (54.0，76.3) years were recruited according to inclusion criteria, among whom 68(28.6%) were female. There were 35 patients (14.7%) in group P with median age of 67.0 (56.0，83.0) years. There were 203 patients（85.3%）in group G with median age of 61.0 (53.0，75.0) years. No significant differences were found in age, sex, body mass index or esophagus cap use（P>0.05）. Indications of abdominal symptoms or digestive system diseases（OR= 2.899，95%CI：1.258-6.681，P=0.012) and PPI use (OR=3.168，95%CI：1.261-7.959，P=0.014) were more likely to yield a low cleanliness score. Gastric preparation regimen with two doses of pronase （OR=0.201，95%CI：0.067~0.603，P=0.004）was more likely to avoid a low cleanliness score. Conclusions Indications of digestive system diseases or abdominal symptoms and PPI use may decrease the cleanliness scores of MCE, while gastric preparation with double doses of pronase may improve it.