To optimize the heat transfer performance of heat exchangers, this study explored the flow properties and heat transfer of cosine-wave-shaped runners with different structural parameters (wave amplitude, focal distance, and circle radius). The effects of the changes in these structural parameters on the flow and temperature fields of specially shaped channels were analyzed. The partial synergy angles of cosine runners were obtained using user-defined programs in CFD software. The synergy of the entire channel was evaluated using the average field synergy angle as an evaluation index. This study investigated the problem of distribution nonuniformity of the temperature differences during the medium flowing process to provide a theoretical foundation and guidelines for optimally designing the structural parameters of specially shaped channels.