In this work, the rotary heat exchanger for waste heat recovery of SCR (Selective Catalytic Reduction) low temperature denitration system in cement kiln is taken as the research background, and a typical heat transfer element in the rotary heat exchanger is selected as the base plate type. The structural improvement methods with different proportions of corrugated height and different corrugated inclination angle are proposed and a series of new-style heat transfer elements are obtained. The flow resistance and heat transfer characteristics of different heat transfer elements are compared and analyzed by three-dimensional numerical simulation method, and the area mass factor j/f is introduced to represent the comprehensive heat transfer performance of the heat transfer elements. The results show that under the same heat transfer condition, the flow disturbance at the boundary layer of the heat transfer element with the corrugated height proportion of 3:1 is gentler than heat transfer elements that of other corrugate height proportion. Therefore, its Nusselt number value is the smallest, the value of the friction coefficient is the smallest, but the area mass factor is the largest. This also proves that the heat transfer element after the adjustment of the corrugated height proportion has improved the comprehensive heat transfer performance compared with the original CU heat transfer element. Under the premise of a heat transfer element with the corrugated height proportion of 3:1, the inclination angle of corrugate is changed in the range of 30°~60°. It is found that, the greater the inclination degree of the heat transfer element, the stronger the flow mixing, the larger the value of the corresponding Nusselt number is, and the larger the value of the friction coefficient is, while the increase of the friction coefficient with the increase of the degree of corrugate inclination is greater than that of the Nusselt number. When the inclination angle of the corrugate is 30°, the comprehensive heat transfer characteristics of the heat transfer element are optimal. The results show that the structure improvement can improve the comprehensive heat transfer performance of flow heat transfer element.