Due to the nanoscale dimensions of the lubricant, overcoat, and media layers, the usual fast and efficient continuum models, such as Fourier law, fail to describe the thermal effects occurring during the heat-assisted magnetic recording (HAMR) operation. Furthermore, in order to couple the local heat transfer to air bearing surface dynamics, thermal energy distribution to the surrounding environment should be understood apart from the heat penetration in the carbon overcoat/media layers. To shed light on this issue, we developed a hybridized multiscale methodology that couples a modified continuum approach that is capable of accommodating nanoscale heat transfer effects, known as Guyer–Krumhansl equation (G–K), with a mesoscale level model based on kinetic theory via lattice Boltzmann method. This modified Fourier equation in G–K form incorporating parameters from the Boltzmann transport equation can accurately capture the nanoscale energy carrier dynamics while retaining the computational efficiency of the conventional models like Fourier law. We investigate the overall heat transfer mechanism originating from the laser hotspot onto the disk via analyzing the disk surface temperature distribution of a realistic media FePt grain surface, as well as the heat loss to the surroundings, including the air bearing environment via convection and radiation. Thus, we obtain a possible design criterion, which relates the grain size to the heat retention in the disk after a pulsing laser is focused. We found out that increasing the grain size may reduce the amount of time the heat is stored in the magnetic layer, thereby increasing the durability of the disk in the HAMR environment. Our study can provide novel design criteria for efficient heat sink materials, for effective thermal management in the disk, as well as improving the media durability via introducing optimized grain structure parameters, including shape and size for preserving lateral temperature gradients at the desired location in the disk during the HAMR operation.