This study was to analyze the diagnostic effects of computed tomography (CT) and magnetic resonance imaging (MRI) in patients with cerebrovascular diseases (CVDs) based on low-rank matrix denoising (LRMD) algorithm. The LRMD algorithm was adopted for MRI diagnosis and CT diagnosis for comparative analysis. 129 CVD patients were selected as the research objects, 43 cases were diagnosed by CT, 43 cases were diagnosed by MRI under LRMD, and the other 43 cases were diagnosed by CT + MRI. The results showed that the diagnostic compliance rates (DCRs) of CT group in the cerebral hemorrhage (CH), cerebral infarction (CI), and cerebral aneurysm (CA) were 95.1%, 94.7%, and 70%, respectively, while those in the MRI group were 99.01%, 97.71%, and 100%, respectively. Thus, it was obtained that MRI diagnosis was much better than CT diagnosis, and CT + MRI showed the best diagnosis efficacy, showing statistical differences ( P < 0.05 ). The accuracy, sensitivity, and specificity of MRI diagnosis under the LRMD algorithm were 96.28%, 88.76%, and 90.62%, respectively, which were superior to those of CT diagnosis (92.71%, 84.94%, and 80.71%, respectively). The diagnosis cost per case (DC/C) (799.73 ± 100.02 yuan) and the total diagnosis cost (TDC) (58,521.67 ± 301.62 yuan) in the MRI group were higher than those in the CT group (601.42 ± 83.61 yuan and 39,819.2 ± 198.72, respectively) ( P < 0.05 ). In conclusion, CT + MRI under the LRMD algorithm showed good potential in diagnosis of CVD; MRI based on the LRMD algorithm showed a higher positive rate in the diagnosis of CA and was better than CT diagnosis, and CT + MRI showed the best diagnosis effect and could improve the clinical diagnosis rate.