Objective To explore the experience of department of healthcare-associated infection(HAI) management in auditing and guiding the layout of painless endoscopy center. Methods Department of HAI management took an active part in the audit and guide of architectural design of painless endoscopy center, fully understood the demand of diagnosis and treatment of clinical departments, investigated the latest domestic and provincial architectural design standards, adopted suitable air-conditioning purification system and decorative material according to the actual situation, through repeated demonstration, the best layout and function of painless endoscopy center was ensured. Results Painless endoscopy center was well designed, reasonably laid out, air was well circulated, and decorative material was suitable, acceptance testing by the third party showed that the indoor air quality was qualified, air colony number conformed to national standard, the overall management of endoscopic instruments has been achieved, subjective feeling of medical staff after use was excellent. Conclusion Department of HAI management intervenes in the audit and guide of architectural layout of painless endoscopy center in advance, which is of great importance for endoscopy center to meet the requirements of relevant standards and increase of its practicability.