Introduction Thyroid cancer is a common malignant tumor, and early diagnosis and timely treatment are crucial to improve patient prognosis. With the increasing use of enhanced CT scans, a new opportunity for early thyroid cancer screening has emerged. However, existing CT-based models face challenges due to limited datasets, small sample sizes, and high noise. Methods To address these challenges, we collected enhanced CT scan image data from 240 patients in Guangdong and Xinjiang, China, and established a CT dataset for early thyroid cancer screening. We propose a deep learning model, the DVT model, which combines transformer DNN and transfer learning techniques to integrate time series data and address small sample sizes and high noise. Results The experimental results show that the DVT model achieves a prediction accuracy of 0.96, AUROC of 0.97, specificity of 1, and sensitivity of 0.94. These results indicate that the DVT model is a highly effective tool for early thyroid cancer screening. Conclusion The DVT model has the potential to assist clinicians in identifying potential thyroid cancer patients and reducing patient expenses. Our study provides a new approach to thyroid cancer screening using enhanced CT scans and demonstrates the effectiveness of deep learning techniques in addressing the challenges associated with CT-based models.