Regeneratively cooled scramjet has already been successfully verified as propulsion device for hypersonic vehicle. As a result, dynamic process of flow and heat transfer in cooling channel is commonly occurred which may bring hazard and control difficulties for scramjet. To study transient flow and heat transfer process in cooling channel, a dynamic numerical model is established. Dynamic characteristics of flow and heat transfer under different conditions are calculated and discussed, which includes change of inlet fuel mass flow, heat flux and pressure working conditions. Results show that stable time of cooling channel outlet fuel temperature is related to the change rate of inlet mass flow and heat flux. The stable time of outlet fuel temperature under heat flux decreasing working conditions are about 12.5 s. The initial response of working pressure fluctuation will lead to fuel temperature fluctuation, which has little effect on wall temperature.