Objective To investigate the role of endoscopic ultrasonography (EUS) in diagnosis and treatment of colorectal submucosal lesions. Methods EUS were applied in 74 patients with suspected colorectal submucosal lesions. According to the origin of submucosal lesion, the patients had received biopsy, endoscopic ultrasonography-fine needle aspiration (EUS-FNA) and endoscopic treatment or surgery. The correlation between EUS and clinical pathology is analyzed retrospectively. Results In the diagnosis based on EUS, there were 28 cases of neuroendocrine tumors (occurred in the rectum), 15 lipomas (4 cases occurred in ileocecal, 1 in transverse colon, 8 in ascending colon, 2 in sigmoid colon), 2 rectal gastrointestinal stromal tumor (1 in muscularis propria and the other in muscularis mucosa), 14 external pressure changes (9 ovarian tumor, 2 lymph nodes, 3 pelvic tumor), 5 cyst (4 in transverse colon, 1 in ascending colon), 1 gas cyst, 3 sigmoid colon endometriosis, 4 rectum malignant tumor invasion, 2 intestinal lymphoma. All the patients had received biopsy, EUS-FNA, endoscopic treatment or surgery. Compared with pathology, a total coincidence rate of 91.9% (68/74) was achieved by EUS, and 2 cases were pathologically diagnosed as leiomyoma, which is considered as rectal carcinoma by EUS at first, 1 case of intestinal lymphoma instead of lipoma, 2 inflammatory mass instead of malignant tumor around the rectum, and 1 rectal carcinoma instead of endometriosis. Conclusion The digestive tract structure could be showed clearly with EUS, and the size of the colon and rectal submucosal lesions, the layer of origin and the structural relationship of adjacent tissues could also be detected. Then, the appropriate treatment against the colon and rectal submucosal lesions would be adopted after the accurate judgment of lesions with EUS.