To enable the long-term use of existing wooden structures, appropriately evaluating the extent of damage of the biodeterioration of structural performance, including members and joint systems, is necessary. To give one example, accurately estimating the single shear strength performance of nail and screw joints with decay is crucial. Therefore, this study proposes a method to model this by dividing wood into multiple layers with different strength performance, considering the grade of deterioration in a cross-section of decayed wood. The model was used to differentiate the sound layer and three decayed layers (multilayer) according to the extent of the damage. The estimated values, which were produced using the proposed model, were compared to the single shear strength of screw and nail joints with decay using two species of wood, namely Abies sachalinensis (Todomatsu) and Cryptomeria japonica (Sugi). The results point to a good fit between the average value of the experimental results and the estimated values of the proposed model. Compared with the existing (single-layer) model, the proposed model improved the accuracy of estimating the strength of wood undergoing early deterioration and therefore was considered usable.