This study aimed to evaluate the value of low-dose dual-input targeted perfusion computed tomography (CT) imaging in the differential diagnosis of benign and malignant pulmonary ground-glass opacity nodules (GGOs).A prospective study was conducted of patients with GGOs who underwent CT perfusion imaging from January 2022 to October 2023. All nodules were confirmed by pathological analysis or disappeared during follow-up. The dual-input perfusion mode (pulmonary artery and bronchial artery) of the body perfusion software was used for postprocessing analysis to measure the perfusion parameters of the pulmonary GGOs. A total of 101 patients with pulmonary GGOs were enrolled in this study, including 43 benign and 58 malignant nodules. The dose length product of the CT perfusion scan was 348 mGy∙cm, which was < 75% of the diagnostic reference level of the chest CT plain scan (470 mGy∙cm). The effective radiation dose was 4.872 mSV. Blood flow (BF), blood volume (BV), mean transit time (MTT), and flow extraction product (FEP) were higher in the malignant nodules than in the benign nodules, with statistically significant differences (p < 0.05). The FEP had the highest accuracy for diagnosis of malignant nodules [area under the curve (AUC) = 0.821, 95% confidence interval (CI): 0.735–0.908], followed by BV (AUV 0.713, 95% CI: 0.608–0.819), BF (AUC 0.688, 95% CI: 0.587–0.797), and MTT (AUC 0.616, 95% CI: 0.506–0.726). When the FEP was ≥ 19.12 mL/100 mL/min, the sensitivity was 91.5% and the specificity was 62.8%. For distinguishing between benign and malignant nodules, the AUC of the combination of BV and FEP was 0.816 (95% CI: 0.728–0.903), and the AUC of the combination of BF, BV, MTT, and FEP was 0.814 (95% CI: 0.729–0.900).Low-dose dual-input perfusion CT was very good at distinguishing between benign and malignant pulmonary GGOs, with FEP exhibiting the highest diagnostic capability.