As an effective means of thermal management, thermal rectification (TR) has been studied in a variety of complex asymmetric or heterogeneous structures. Due to experimental conditions, many complex structures cannot be realized easily, and the low-temperature thermal bath temperature far below room temperature does not conform to the actual application environment of the device. In this paper, we studied the thermal rectification inside graphene supported by a heterogeneous substrate of SiO2 and GaN alternately. Heat flux is easier to transfer from the graphene covered on the SiO2 side to the GaN side. When the temperature of the cold bath is maintained at 300 K, only the temperature of the high-temperature hot bath is changed, and the maximum TR rate is about 52%. TR rate can be tuned by heat source temperature and size, with heat source size of 2 nm and temperature above 450 K, the highest TR rate can be obtained. The phonon density of states and participation ratio reveal the influence of the substrate and position on the phonon transport in graphene. Besides, the spectral energy density analysis confirmed that the substrate effect caused the shift of the graphene flexural phonon mode and the reconstruction of the phonon spectrum, which was in good agreement with PDOS, and further explain the basic mechanism of TR from the scattering rate and the degree of localization.