To observe the microstructural longitudinal alterations in neural tissues after ischemic stroke and assess the correlation with clinical outcome and NODDI metrics. 18 subjects were enrolled. Intra-cellular volume fraction(Vic) and orientation dispersion index(OD) exhibited positive correlations with NIHSS scores of patients at day 30. The correlation of the susceptibility with the NODDI metrics and prognosis is higher than the ADC values with it. NODDI may provide a more promising and reliable methods for microstructural reorganization follow-up stroke than other measures previously used in studies of stroke recovery.