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Characterization of the adhesive penetration behavior in wood is highly desired for optimizing the manufacturing processes and product properties. In this study, modified urea-formaldehyde (UF) adhesive was used to prepare glued laminated timber (Cryptomeria fortunei Hooibrenk). The depth of gross penetration was measured by fluorescence microscopy (FM), which showed the UF passed through 1.5 to 3.5 earlywood tracheids (with an average penetration depth of 88.95 ± 27.49 μm) or 0.5 to 4.0 latewood tracheids (with an average penetration depth of 36.39 ± 15.14 μm). In addition, the distribution of cell wall penetration was observed clearly by confocal laser scanning microscopy (CLSM). The adhesive was found to diffuse into the cell walls of surface tissues embedded in the UF. To verify the results from CLSM, the mechanical properties of cell walls with and without adhesive penetration were measured through nanoindentation (NI). The reduced elastic modulus of exposed cell walls (18.10 GPa) was roughly equal to that of fully filled cell walls (17.68 GPa) but significantly greater than that of reference ones (15.71 GPa). The hardness showed a similar variation trend for these three types of cell walls. Combining the three techniques, both the microstructure and micromechanics of the adhesive penetration behavior can be quantitatively identified in a complementary manner.