This study was to use the partial differential mathematical model to analyze the magnetic resonance imaging (MRI) images of cerebral ischemia-reperfusion injury (CIRI) and to dynamically observe the role of L-theanine in CIRI based on this. 30 patients with cerebral ischemia in a hospital in a certain area were selected and divided into a cerebral ischemia group and a L-theanine treatment group. The two groups of patients were examined by MRI within 48 hours, and the relative apparent diffusion coefficient (rADC) of the cerebral ischemic part of the patients was determined. The partial differential mathematical model was used for data processing to obtain the function of cerebral ischemia time and infarct area, and the data of patients in the cerebral ischemia group and L-theanine treatment group were compared and analyzed. The results showed that the partial differential mathematical model could effectively analyze the linear relationship between the rADC value and time in the treatment of CIRI using L-theanine. The rADC values of the four points of interest in the L-theanine treatment group all increased with time, and there was a positive correlation between the variables X and Y. In observing the efficacy indicators of L-theanine, the L-theanine treatment group showed a significant advantage in the neurospecific enolase (NSE) content compared with the cerebral ischemia group (P < 0.01), and the neurological function score of the L-theanine treatment group gradually decreased and showed a statistically obvious difference on the 7th day of treatment (P < 0.05). In summary, it was verified in this study that the role of L-theanine in the treatment of CIRI was of a great and positive significance for the subsequent treatment of patients with cerebral ischemia, providing reliable theoretical basis and data basis for clinical treatment of CIRI.