Predicting the depth of invasion of superficial esophageal squamous cell carcinomas (SESCCs) is important when selecting treatment modalities such as endoscopic or surgical resections. Recently, the Japanese Esophageal Society (JES) proposed a new simplified classification for magnifying endoscopy findings of SESCCs to predict the depth of tumor invasion based on intrapapillary capillary loops with the SESCC microvessels classified into the B1, B2, and B3 types. In this study, a four-step classification method for SESCCs is proposed. First, Niblack’s method was applied to endoscopy images to select a candidate region of microvessels. Second, the background regions were delineated from the vessel area using the high-speed fast Fourier transform and adaptive resonance theory 2 algorithm. Third, the morphological characteristics of the vessels were extracted. Based on the extracted features, the support vector machine algorithm was employed to classify the microvessels into the B1 and non-B1 types. Finally, following the automatic measurement of the microvessel caliber using the proposed method, the non-B1 types were sub-classified into the B2 and B3 types via comparisons with the caliber of the surrounding microvessels. In the experiments, 114 magnifying endoscopy images (47 B1-type, 48 B2-type, and 19 B3-type images) were used to classify the characteristics of SESCCs. The accuracy, sensitivity, and specificity of the classification into the B1 and non-B1 types were 83.3%, 74.5%, and 89.6%, respectively, while those for the classification of the B2 and B3 types in the non-B1 types were 73.1%, 73.7%, and 72.9%, respectively. The proposed machine learning based computer-aided diagnostic system could obtain the objective data by analyzing the pattern and caliber of the microvessels with acceptable performance. Further studies are necessary to carefully validate the clinical utility of the proposed system.