BackgroundPrevious studies using emerging diffusion MRI techniques have revealed damage to the white matter (WM) microstructure in amyotrophic lateral sclerosis (ALS), particularly the influence of crossed fibers, but there is a lack of subgroup analyses.PurposeTo detect WM microstructural changes in ALS patients using fixel‐based analysis (FBA) and neurite orientation dispersion and density imaging (NODDI) MRI.Study TypeProspective.PopulationThirty‐six ALS patients (aged 60.50 ± 9.5 years) and 25 healthy controls (HCs) (aged 58.90 ± 8.1 years).Field Strength/Sequence3 T; NODDI and FBA (b‐values = 0, 1000, and 2500 seconds/mm2).AssessmentSubgroups were performed according to progression rate and cognition, including fast and slow progression (FP/SP), ALS with and without cognitive impairment (ALS‐ci/ALS‐nci). Fiber density (FD), fiber‐bundle cross‐section (FC), combined fiber density and cross‐section (FDC), neurite density index (NDI), orientation dispersion index (ODI), isotropic volume fraction (ISO), and fractional anisotropy (FA) were calculated and their correlation with clinical variables examined.Statistical TestingChi‐square test, Mann–Whitney U test, two‐sample t test, partial correlation analysis, and false discovery rate (FDR) corrected. A P‐value <0.05 was considered significant.ResultsALS patients had lower FD and FDC values predominantly in the corticospinal tract (CST) and corpus callosum (CC) regions, as well as lower NDI value in the CC, radial crown, and internal capsule compared to HCs. Subgroup analysis based on progression rate and cognitive function showed significant differences in FBA results. The FC in the right CST region was significantly lower in the FP than SP, and the FD in the CC region was significantly lower in the ALS‐ci than ALS‐nci. Furthermore, a negative correlation was found between the mean FC value and the rate of progression in ALS patients (r = −0.408).Data ConclusionFBA is a powerful tool for detecting complex cerebral WM microstructural damage for evaluating ALS cognition and disease progression.