Quantitative morphological traits may be defined based on the 3D anatomy reconstructed from micro X-ray computed tomography (μCT) images. In this study, the heterogeneous spatial distribution of trichomes (hairs) on the adaxial leaf blade surface in Arabidopsis was evaluated in terms of 3D quantitative traits, including trichome number, average nearest-neighbour distance between trichomes, and proportion of large trichomes. The data reflect spatial heterogeneity in the radial direction, in that a greater number of trichomes were observed on the leaf blade margins relative to the non-margins, a distribution effect caused by the CAPRICE (CPC) and GLABRA3 (GL3) genes, which have previously been shown to affect trichome density. We further determined that the proportion of large trichomes on the blade mid-rib increases from the proximal end to the distal leaf tip in both wild-type plants and GL3 mutants. Our results indicate that the GL3 gene affects trichome distribution, rather than trichome growth, causing trichome initiation at the proximal base rather than the distal tip. On the other hand, CPC does affect trichome growth and developmental progression. Hence, quantitative phenotyping based on μCT enables precise phenotypic description for elucidation of gene control in morphological mutants.