Objective To determine the independent influencing factors of intraoperative choking during painless gastrointestinal endoscopy (PGIE) after coronavirus disease 2019 (COVID-19). Methods The data of patients undergoing PGIE with COVID-19 in Northern Jiangsu People’s Hospital between December 2022 and April 2023 were retrospectively collected. Multiple logistic regression analysis was used to screen the influencing factors of intraoperative coughing events that occurred during the diagnosis and treatment process. Results A total of 948 patients were included, with 93 (9.8%) cases of choking. The results of the multiple logistic regression analysis showed that smoking and unresolved cough were independent risk factors for coughing (P<0.05), while colonoscopy and infection duration beyond 14 days between diagnosis and treatment were independent protective factors for coughing (P<0.05). ConclusionsWhen patients with COVID-19 undergoing PGIE, special attention should be paid to high-risk groups such as smoking and unresolved cough. It is necessary to strengthen intraoperative monitoring and implementation of prevention and control measures to reduce the incidence of coughing and improve the safety of diagnosis and treatment for patients.