A method for measuring thermal diffusivity of orthotropic materials by using multidimensional heat transfer model combined with parameter estimation is proposed. The unsteady mathematical model of three-dimensional temperature field is established by heat conductivity product method, the thermal diffusivity is calculated by random conjugate gradient method, and the thermophysical property testing system is developed. The constant-temperature boundary is constructed by using a constant-temperature water bath box combined with graphene stickers wrapped on the surface of the sample, the insulation material covers the upper surface of the sample to construct an insulating boundary, and thermocouples are arranged on the upper surface to monitor the temperature rise change. First, isotropic materials, such as acrylic plate and marble, were tested. Compared with a reference value, the maximum relative deviation of thermal conductivity was 3.72%, which verified the feasibility and accuracy of the test method. Furthermore, the orthotropic-material unidirectional carbon fiberboard was tested. Compared with the results measured by improved parallel hot-wire method, the relative deviations of thermal diffusivity, thermal conductivity, and specific heat capacity were 3.66, 1.59, and 2.15%, respectively, which indicate that this test method could meet the thermophysical testing requirements of orthotropic materials.