For decades, ultrasound images have been widely used in the detection of various diseases due to their high security and efficiency. However, reading ultrasound images requires years of experience and training. In order to support the diagnosis of clinicians and reduce the workload of doctors, many ultrasonic computer aided diagnostic systems have been proposed. In recent years, the success of deep learning in image classification and segmentation has made more and more scholars realize the potential performance improvement brought by the application of deep learning in ultrasonic computer-aided diagnosis systems. This study is aimed at applying several machine learning algorithms and develop a machine learning method to diagnose subcutaneous cyst. Clinical features are extracted from datasets and images of ultrasonography of 132 patients from Hunan Provincial People’s Hospital in China. All datasets are separated into 70% training and 30% testing. Four kinds of machine learning algorithms including decision tree (DT), support vector machine (SVM), K -nearest neighbors (KNN), and neural networks (NN) had been approached to determine the best performance. Compared with all the results from each feature, SVM achieved the best performance from 91.7% to 100%. Results show that SVM performed the highest accuracy in the diagnosis of subcutaneous cyst by ultrasonography, which provide a good reference in further application to clinical practice of ultrasonography of subcutaneous cyst.