Microstructures in biological tissues can produce susceptibility related microscopic background gradient (μBG). Mapping the spatial distributions of μBG can help us infer tissue microstructure. In this study, we reported an improved diffusion MRI based method to detect μBG and evaluated the method using a phantom as well as normal and dysmyelinated mouse brains. We found that 3D spatial variations of μBG were greater in white matter tracts than in gray matter structures. The contrast based on μBG spatial variations was able to distinguish white matter tracts in normal and dysmyelinated mouse brains. The method may be used to study myelin injury.