On the basis of cooling mechanisms and its factors of crushed rock layer widely used in the Qinghai–Tibet railway, a new hollow concrete brick layer is proposed for the Qinghai–Tibet freeway. A high-precision macro wind velocity detector was employed to study the natural convective characteristics of both types of rock layers and their differences. The natural convection velocity in both types of rock layers resulting from the temperature difference was investigated for the first time through modeling experiment. Natural convection velocity in the hollow concrete brick layer with weak convection resistance was higher than that in the crushed rock layer. Their maximum velocities were 0.10m/s and 0.08m/s, respectively. The different heat transfer processes and their intensities resulting from the boundary temperature fluctuations were the primary reasons for inner asymmetric temperature fluctuation and decline. The cooling process closely related to convection time and convection velocity. The temperature difference was the key factor in the occurrence of convection and its intensity change, although the air temperature changes also had an effect on the airflow process. The occurrence of natural convection required a start-up temperature difference. Moreover, a linear relationship was observed between natural convection velocity and temperature difference.