Objective To analyze general information, diagnosis and treatment of digestive endoscopy departments in county-level hospitals of Yunnan Province, thus to provide evidence for improving the endoscopic diagnosis and therapy in these hospitals. Methods An online survey was performed to collect quality-related information of digestive endoscopy centers (departments) at county-level hospitals of Yunnan from January 2019 to January 2020, including endoscopic equipment, endoscopic techniques, staffing, number of operations, and quality control. Results A total of 143 county-level hospitals were involved in this study. Each hospital owned only 1.74 endoscopy operation rooms on average, 1.42 regular endoscopy workstation, 4 endoscopes. There were only 10 endoscopic ultrasonography workstations and 2 enteroscopy workstations respectively installed in these hospitals. Endoscopic retrograde cholangiopancreatography was independently performed in only 4 hospitals. There were 392 professional endoscopists in all 143 hospitals, 18.62% (73/392) of whom were able to perform endoscopic therapy of grade 4, while only 6.12% (24/392) of whom could perform endoscopic submucosal dissection (ESD) independently. In 2019, the early diagnostic rate of gastrointestinal tract cancer in these hospitals was 19.48% (1 133/5 817). The early diagnostic rate was 21.04% (276/1 312) for esophageal cancer, 19.53% (397/2 033) for gastric cancer, and 18.61% (460/2 472) for colorectal cancer. The colorectal adenoma detection rate was 12.83% (12 207/95 148). The rate of reaching cecum during colonoscopy was 70.49% (67 067/95 148). The complete resection rate of ESD was 12.54% (221/1 763). Conclusion The general situation of digestive endoscopy in county-level hospitals of Yunnan is far from being well-developed, which may be attributed to slow upgrading of equipments, inadequate training of endoscopic professionals and undemanding quality control. It is highly significant to improve medical service and quality of diagnosis and treatment of digestive endoscopy in these hospitals, on the basis of a complete endoscopy quality control system with a high standard.