Regeneratively cooled scramjets are successfully used as propulsion devices in hypersonic vehicles. During operation, scramjets experience acceleration. This special process causes a dynamic flow process, and heat transfer in the cooling channel commonly occurs, which may cause hazards and control difficulties for scramjets. A dynamic numerical model with a modified heat transfer coefficient calculation method was established to study the transient flow and heat transfer processes in a cooling channel. The dynamic characteristics of the flow and heat transfer under different conditions were calculated and are discussed, including the changes in the inlet fuel mass flow, heat flux, and pressure working conditions. The results indicate that the stable time of the cooling channel outlet fuel temperature is related to the rate of change in the inlet mass flow and heat flux. The stable time of the outlet fuel temperature under decreasing heat flux working conditions was approximately 12.5 s. These results summarize the dynamic flow and heat transfer characteristics, which are significant for designing cooling channels in scramjets.