The ultimate properties of a fibrous composite system depend highly on the transverse mechanical properties of the fibers. Here, we report the size dependency of transverse elastic modulus in cellulose nanocrystals (CNCs). In addition, the mechanical properties of CNCs prepared from wood and cotton resources were investigated. Nanoindentation in an atomic force microscope (AFM) was used in combination with analytical contact mechanics modeling (Hertz model) and finite element analysis (FEA) to estimate the transverse elastic moduli (Et) of CNCs. FEA modeling estimated the results more accurately than the Hertz model. Based on the AFM–FEA calculations, wood CNCs had higher transverse elastic moduli in comparison to the cotton CNCs. Additionally, Et was shown to increase with a reduction in the CNCs’ diameter. This size-scale effect was related to the Iα/Iβ ratio and crystalline structure of CNCs.