Objective To discover the relationship between colonoscopy specimens, carcinoembryonic antigen (CEA) combined with cancer antigen 125 (CA125) and postoperative pathological findings of colon cancer. Methods A total of 88 suspected cases of colon cancer were selected and examined from July 2015 to July 2017. The relationship of the specimens collected by colonoscopy, CEA and CA125 levels were analyzed to determine their accuracy towards pathological results. Results The proportions of malignancy parts of pathologic findings were 64.52%, 63.64%, 61.54%, 80%, 71.43%; the total proportion of malignancy was 67.05%; the sensitivity, specificity, missed diagnosis, accuracy, positive predictive value and negative predictive value of colonoscopy in the diagnosis of colon cancer were 76.36%, 45.45%, 23.64%, 64.77%, 70.00% and 53.57%, respectively. The sensitivity, specificity, missed diagnosis, accuracy, positive predictive value and negative predictive value of CEA combined with CA125 in the diagnosis of colon cancer were 88.14%, 79.31%, 11.86%, 85.23%, 89.66% and 76.67%, respectively. CEA and CA125 levels of malignant lesions were significantly higher than those of benign lesions (P < 0.05). Conclusions CEA and CA125 have high accuracy in the diagnosis of early colon cancer patients, and the increase of their clinical expression level is positively correlated with the malignant degree of cancer. Therefore, in order to further improve the accuracy of the examination of early colon cancer patients, it is suggested to use colonoscopy combined with CEA and CA125 levels to diagnose colon cancer, so as to realize early detection and treatment, which is worthy of clinical reference.