Objectives: The aim of this study was to make a reasonable and accurate assessment of the prognosis of patients with pontine infarction. We assessed the changes in structure and function in the whole brain after pontine infarction from the acute to chronic phase using diffustion tensor imaging and functional magnetic resonance imaging. Materials and methods: Sixteen individuals with a recent pontine infarction and sixteen healthy controls were recruited and underwent 3.0T DTI, resting-state fMRI and upper extremity Fugl-Myer (UE-FM) functional evaluation at five time points: within one week (T1), half a month (T2), one month (T3), three months (T4), and six months (T5) after onset. Tract-based spatial statistics was used to conduct a voxelwise analysis. Results: The fractional anisotropy (FA) values were significantly lower in the pontine infarction group than in the control group. Then, specific ROIs were analyzed. The FA values of 10 regions of interest were significantly increased at T2 compared with those at T1. The FA value of the corticospinal tract was significantly increased at T3 compared with that at T2. Regional brain activity results showed that the amplitude of low frequency fluctuations value of the frontal lobe decreased at T1, then increased. Finally, The UE-FM scores showed the same increased trend. Conclusion: These findings show that the microstructure changes most significantly within half a month after pontine infarction and stabilizes after one month. The recovery of motor function in the later period is mainly caused by changes in the cortex. This facilitates more treatment options.