Wood is an anisotropic material that has non-identical properties in different structural directions. Due to its particularly biological characteristics, wood is susceptible to moisture degradation. To better understand the hygrothermal performance of wooden products in buildings and reduce moisture-induced deteriorations, a complete hygrothermal measurement of oak and spruce in three structural directions is carried out. The oriented-dependent moisture transport characteristics are acquired from water vapor transmission, drying, and water absorption tests. The anisotropic properties of both wood species are characterized, and their impacts are further investigated by studying the thermal and moisture behaviors of spruce and oak beams embedded in the wall assemblies interiorly insulated by the calcium silicate and mineral wool insulation systems. Hygrothermal simulations performed by the 2D and 3D models with the isotropic property are compared with those of the 3D models with the anisotropic property. The results show that the 3D hygrothermal models with the anisotropic property can properly represent the heat and moisture conditions of wooden beams. The longitudinal property yields a similar hygrothermal performance of the wooden beam to the anisotropic property. For simplification, the longitudinal property can replace the anisotropic property of wood in the 3D model of the wall assemblies to assess the moisture deterioration risk with sufficient accuracy.