Three-dimensional (3D) high-resolution imaging can help us better understand the brain, and CUBIC is a powerful technique to render the brain transparent, thus benefiting 3D imaging. In this study, we combined CUBIC with immunofluorescence staining (IFS) and successfully acquired 3D high-resolution images of cerebral vessels, astrocytes, dopaminergic neurons and pericytes, providing us abundant information about the change in spatial frequency content for cellular scale features. Additionally, we found that a longer duration of antibody incubation produced deeper staining. Our study indicates the broad application prospects of IFS-based CUBIC for studying specific cerebral structures and diseases related to alterations of these structures.