Poly(methyl methacrylate) (PMMA) is commonly used for dental dentures, but it has the drawback of promoting oral health risks due to oral bacterial adhesion. Recently, various nanoparticles have been incorporated into PMMA to tackle these issues. This study aims to investigate the mechanophysical and antimicrobial adhesive properties of a denture resin by incorporating of nanoclay into PMMA. Specimens were prepared by adding 0, 1, 2, and 4 wt % surface-modified nanoclay (Sigma) to self-polymerizing PMMA denture resin. These specimens were then evaluated using FTIR, TGA/DTG, and FE-SEM with EDS. Various mechanical and surface physical properties, including nanoindentation, were measured and compared with those of pure PMMA. Antiadhesion experiments were conducted by applying a Candida albicans (ATCC 11006) suspension to the surface of the specimens. The antiadhesion activity of C. albicans was confirmed through a yeast-wall component (mannan) and mRNA-seq analysis. The bulk mechanical properties of nanoclay-PMMA composites were decreased compared to those of pure PMMA, while the flexural strength and modulus met the ISO 20795−1 requirement. However, there were no significant differences in the nanoindentation hardness and elastic modulus. The surface energy revealed a significant decrease at 4 wt % nanoclay-PMMA. The antiadhesion effect of Candida albicans was evident along with nanoclay content in the nanocomposites and confirmed by the reduced attachment of mannan on nanoclay-PMMA composites. mRNA-seq analysis supported overall transcriptome changes in altering attachment and metabolism behaviors on the surface. The nanoclay-PMMA materials showed a lower surface energy as the content increased, leading to an antiadhesion effect against Candida albicans. These findings indicate that incorporating nanoclay into PMMA surfaces could be a valuable strategy for preventing the fungal biofilm formation of denture base materials.