Experiencing several earthquakes around the world indicate that, for a specific earthquake, the amount of structural damages, with almost identical features, is highly influenced by the condition of the site, which is called as the site effects. In fact, something which exists in reality and practice is, in most cases, the non-prismatic canyons in line with the longitudinal axis of the valley so that narrowing parts of the canyons are usually selected as the appropriate sites for a variety of structures, and then studied .In this study, the dynamic behavior of prismatic and non-prismatic canyons, using three-dimensional boundary element method in triangular, trapezoidal, and semi-circular forms under the SH waves, are studied. The Results indicate that the movement of non-prismatic canyons, which have narrowing in the middle and opening in two ends of the canyon, based on the frequency and wave angle, are in some cases more than prismatic canyon. Therefore, to obtain accurate values of site effects, it is necessary to do a realistic and three-dimensional modeling of the canyon.