The purpose of this study was to explore cerebral structural and functional changes in amyotrophic lateral sclerosis (ALS) patients with or without dysphagia compared with healthy adults. In total, five ALS patients with dysphagia, five ALS patients without dysphagia and 10 healthy controls were evaluated using diffusion tensor magnetic resonance imaging (DTI) and event-related functional magnetic resonance imaging (fMRI) while laryngeal swallow-related movements were recorded. The fMRI data were analysed using the general linear model to gain the differential statistical map (two-sample t-test) for each group. Maps of fractional anisotropy (FA) and mean diffusivity (MD) were calculated within the masks that corresponded to the different statistical functional maps of intergroup comparisons. During the voluntary saliva swallowing, prominent activation of foci corresponded to the primary sensorimotor (SM) cortex in both ALS and controls, while decreased activation of the SM cortex was observed in ALS patients with dysphagia. DTI analysis revealed that FA was significantly reduced and MD was typically increased in the posterior limb of the internal capsule, thalamus, and anterior cingulate gyrus, as well as in the insula of ALS patients compared with controls. However, in ALS patients with dysphagia, FA and MD were more sensitive to these changes than ALS patients without dysphagia. This study highlights the potential of DTI and fMRI for monitoring structural degeneration and functional changes in patients with ALS. This study is the first to demonstrate that cerebral activation map changes correspond to distribution patterns of diffusion abnormalities. Combined non-invasive neuroimaging techniques may be useful tools to assess prognosis and study rehabilitation strategies for dysphagic ALS patients, especially for patients who are MRI-negative by conventional methods.