Objective: To evaluate the effectiveness of deep learning model trained on routine CT scans when identity the malignant and benign lung nodule on target CT scans dataset. Methods: This retrospective study enrolled 923 patients with lung nodules found by chest CT scan in Shanghai Chest Hospital from January 2016 to December 2018. A total of 969 nodules with pathological report were analyzed. The deep learning based pulmonary malignant prediction method in a fine-grained classification manner was used to make the prediction, and the AUC (the area under the curve), accuracy, sensitivity and specificity of routine CT scans and target CT scans were compared, and Delong test and IDI (Integrated Discrimination Improvement) were employed to provide statistical results. Furthermore, statistical methods were used to investigate the differences between the benign and malignant classification of nodules on routine CT and on target CT. Results: In the benign and malignant discrimination task, AUC, accuracy, sensitivity and specificity on the routine scans were 0.81, 82.0%, 86.0% and 56.6% respectively, while the AUC, accuracy, sensitivity and specificity on the target scans were 0.84, 85.0%, 88.8% and 60.5% respectively. The IDI was 0.056 (Z test, P<0.05), and there was statistically significant difference in ROC (Delong test, P=0.01). Conclusions The deep learning model trained on the data set of routine CT scans can achieve better diagnostic efficiency in target CT scans data.