Graphene exhibits high carrier mobility and concentration as well as other remarkable properties. Among them, the thermal behaviors of phonon modes play important roles in the application of optical and electronic devices. Here, A–A stacked graphene were proved well by Raman investigation on G and 2D modes. Temperature-dependent Raman scattering measurements on graphene with various number of layers on different substrates were conducted in the temperature range of 80–460 K. The first-order temperature coefficient of single layer graphene (SLG) on SiO2/ Si substrate is obviously smaller than that on Cu foil, indicating that the substrate effect attributes a great impact on graphene phonon temperature dependence. The first-order temperature coefficients of multilayer graphene linearly decrease as the number of layers increases, attributed to the reduction of substrate effect in phonon behaviors, rather than to the anharmonic phonon–phonon (ph–ph) coupling or thermal expansion.