High-Altitude Platform Station (HAPS) is one of the promising wireless communication infrastructures in the future. The major factor affecting its communication channel is environment. An accurate characterization of shadowing caused by the environment is needed for this new wireless infrastructure. This paper is, therefore, designed to address and evaluate the shadowing characteristics from urban physical structures for HAPS communications. Experiments are first conducted in urban areas of Japan and then we present the results of shadowing characteristics at various conditions in each specific area. Second, an analytical model is developed to evaluate the shadowing condition for HAPS channel based on the environmental characteristic data derived from the experimental areas and a geometrical model. Finally, comparisons between empirical studies and the analytical model are made. The comparison results show that the proposed analytical model is reliably practical in characterizing shadowing in urban areas by using the environmental statistical data and the geometrical model.