Heat-assisted magnetic recording (HAMR) is one of the most promising techniques to extend the recording density in hard disk drives beyond 4 Tb/in <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> . This places a range of stringent operating requirements in the head disk interface, including heating and cooling of the media, must occur within the order of nanosecond in order to achieve the necessary data rates, generate a large thermal gradient for sharp bit edge, and ensure that the recorded data are thermally stable during cooling to ambient. Optical energy must be efficiently delivered and confined to a spot in the medium that is much smaller than the diffraction limit so that neighboring tracks are not heated. To shed light on this issue, a mesoscale level model based on kinetic theory called lattice Boltzmann method (LBM) is applied to understand the nanoscale heat transfer in the media layer in HAMR operations. In this paper, we examine the effects of main energy carriers at nansocale (electrons and phonons) via novel LBM-based methodology. We investigate the overall heat transfer contribution of the coupled heat carriers and the electron-phonon coupling issues in the carbon matrix and media grain interface in a representative FePt media layer. Since thermal gradients and grain size are very important for achieving high-density HAMR recording, the in-plane crosstrack temperature gradients of structural effects with two representative grain shapes (hexagonal and circular) and sizes (10 and 5 nm) are investigated. We observed that 10 nm grains of both shapes show lower temperature gradients compared with the 5 nm size, due to the increase of carrier scattering at the grain/carbon matrix interface. Circular grain shape produces larger temperature gradient magnitude compared with hexagonal grain structure. Thus, this paper will produce insight in the mechanism to control the thermal management and temperature gradients for high-density HAMR.