In carbon fiber reinforced plastic adhesive joints, poor adhesion caused by weak bonds may occur because of contamination at the bond line. Weak bonds were reproduced using molecular dynamics simulations to investigate their mechanisms. Furthermore, weak-bond models were created by incorporating water, xylene, and silicone molecules as contaminants into two epoxy models. Tensile and shear analyses were performed to evaluate the mechanical properties of the weak-bond models. The results revealed that the addition of the contaminants reduced the strength of the models. Stress concentration occurred because of the presence of the inserted molecules at the bond line. To consider these results, density and free-volume distributions were evaluated. The molecular size of a contaminant influences its distribution in the epoxy model, thereby affecting the mechanical properties of the model.