In this study a numerical simulation model that integrates hygrothermal analysis with the decaying process of wood structures caused by moisture accumulation is presented. This simulation model can quantitatively predict both hygrothermal conditions within the building envelopes and the progress of decay in wood structures under variable conditions. The following are characteristics of the simulation model used in this study: (1) the development of wood decay represented by a differential equation with a variable of mass loss of wood substance and (2) the addition into moisture balance equations of biochemical reactions within wood decay. Hence, the simulation model enables assessment of the long-term performance of building envelopes with regard to both durability and drying potential. Rate constants of the wood decay and a coefficient of the moisture production for the model were determined by the mass loss data of small wood samples in decay tests using Fomitopsis palustris, a brown rot fungus. Additionally, numerical simulations using the model were implemented to understand both the decaying process and moisture accumulation within building envelopes. The results numerically demonstrated important phenomenon that the moisture production by biochemical reactions of wood decay helps to maintain the decaying process.