A 3-D elastic finite element model was developed to investigate the stresses distribution of bi-adhesive bonded joints (i.e., the bond line of joints filled with two adhesives of dissimilar toughness). The effects of the loading mode on the stress distribution of joints, including the single-lap joints under tensile loading (i.e., single-lap joints) and the butt joints under cleavage loading (i.e., cleavage joints), were also studied in detail. Results showed that higher stress, distributed at the contact position of the dissimilar adhesives placed along the bond line of bi-adhesive bonded joints. Also, the maximum stress of the adhesive layer decreased when the length ratios and bonding sequence along the bond line, filled with two dissimilar adhesives, was appropriately designed. At the same time, stress convergence in the adhesive layer of bi-adhesive joints was also obviously reduced in contrast to the mono-adhesive joints. The numerical investigation shows that it is necessary to take into account the change of loading modes when optimizing the bi-adhesive joint design, because of the uneven and complex loading modes of the adhesive bonding structure in the engineering applications.