Objective To investigate the effect of low dose MSCT on thyroid benign and malignant nodules. Methods From June 2014 to December 2016, 84 patients with thyroid nodular lesions admitted in our hospital were divided into benign group (n=70) and malignant group (n=14). The parameters of BF, BV, TTP, MTT and so on were calculated by CT scan and stratified dynamic perfusion scan. Results The MSCT features of the benign group were mainly nodular shape, with clear margins and granular calcification. The MSCT features of the malignant group were irregular nodules, blurred and granular calcification. The MSCT features of the two groups were (P<0.05), patients with benign thyroid nodules after intensive scan, the specific performance of uniform enhancement, 8.6% of patients showed complete ring enhancement, thyroid nodular malignant patients after intensive scan, the specific performance of the tumor (P<0.05). The levels of TTP and MTT in patients with malignant thyroid nodules were (24.69±1.74) s, (10.51±0.31) s, respectively, and there was significant difference between the two groups (P<0.05). Conclusion The low dose of TTP and MTT in patients with benign thyroid nodules were significantly lower than those in benign thyroid nodules (30.14±7.65) s and (17.26±11.65) MSCT perfusion imaging can be a certain extent to respond to patients with thyroid class hemodynamic conditions, reduce the amount of radiation by patients, for the diagnosis of thyroid benign and malignant nodules have a certain reference use.