Improving the billet temperature uniformity is crucial for the quality of rolled products. This paper investigated the heat and mass transfer processes in a regenerative reheating furnace by establishing typical heating unit models. The periodic combustion switching and misaligned water-cooled beams were considered. The effects of furnace temperature oscillation and skid marks on the total heat transfer coefficient distribution and billet temperature uniformity were analyzed. The results indicate that during the heating process of the billet, the periodic variation amplitude of furnace temperature decreases from 86 to 25 °C, and the depth of influence on the billet temperature is about 0.03 m. The total heat transfer coefficient on the billet bottom surface shows a wave distribution affected by beams shielding, but on the top surface, the closer it is to the furnace wall, the smaller the total heat transfer coefficient. The misalignment of water-cooled beams effectively eliminates the original skid mark and reduces the range of new skid mark. However, the cross-sectional temperature difference at the new skid marks remain at about 97 °C. Compared to extending the residence time, increasing the furnace temperature in the soaking zone is the optimal measure to reduce the influence of skid marks.