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Abstract Background In this study, images of 2450 benign thyroid nodules and 2557 malignant thyroid nodules were collected and labeled, and an automatic image recognition and diagnosis system was established by deep learning using the YOLOv2 neural network. The performance of the system in the diagnosis of thyroid nodules was evaluated, and the application value of artificial intelligence in clinical practice was investigated. Methods The ultrasound images of 276 patients were retrospectively selected. The diagnoses of the radiologists were determined according to the Thyroid Imaging Reporting and Data System; the images were automatically recognized and diagnosed by the established artificial intelligence system. Pathological diagnosis was the gold standard for the final diagnosis. The performances of the established system and the radiologists in diagnosing the benign and malignant thyroid nodules were compared. Results The artificial intelligence diagnosis system correctly identified the lesion area, with an area under the receiver operating characteristic (ROC) curve of 0.902, which is higher than that of the radiologists (0.859). This finding indicates a higher diagnostic accuracy (p = 0.0434). The sensitivity, positive predictive value, negative predictive value, and accuracy of the artificial intelligence diagnosis system for the diagnosis of malignant thyroid nodules were 90.5%, 95.22%, 80.99%, and 90.31%, respectively, and the performance did not significantly differ from that of the radiologists (p > 0.05). The artificial intelligence diagnosis system had a higher specificity (89.91% vs 77.98%, p = 0.026). Conclusions Compared with the performance of experienced radiologists, the artificial intelligence system has comparable sensitivity and accuracy for the diagnosis of malignant thyroid nodules and better diagnostic ability for benign thyroid nodules. As an auxiliary tool, this artificial intelligence diagnosis system can provide radiologists with sufficient assistance in the diagnosis of benign and malignant thyroid nodules.