<p>This work investigates the vibrational behavior of an adatom-microstructure system under the combined effects of thermal loading, adatom adsorption, and nonlocal strain gradient phenomena. The dynamic response is evaluated under both uniform and nonlinear thermal loads, providing novel insights into how thermal environments influence the system’s behavior, which has been overlooked in previous studies on similar structures. The investigated structure is a sandwich-type microbeam whose core contains periodic square perforations spread along its axis, and top and bottom face sheets made of functionally graded porous materials (FGP) with even porosity distribution. The properties of the materials are graded across thickness using a power-law function. The study employs the nonlocal strain gradient elasticity theory (SGET), which includes two independent scale parameters corresponding to both strain gradient and nonlocal effects, to represent small-scale phenomena, while the interactions between adatoms and the microstructure substrate, as well as between adatoms themselves, are captured by van der Waals forces, represented through the Lennard-Jones potential (6–12). To determine the system’s resonance frequency, modified vibration equations based on the Euler–Bernoulli beam model (EBM) and Levinson beam model (LBM) were developed. These were resolved using the Navier solution method (NTM) and the differential quadrature method (DQM). The frequency shift for the H/Si(100) system was computed, with numerical results indicating that the shift response was affected by a variety of parameters, including porosity, thermal loading, perforation geometry, adatom presence, the material’s power-law gradient, and nanoscale impacts. The study provides novel insights into how multiphysics parameters influence the system’s dynamic response. These results are crucial for the design and development of M/NEMS-based mass sensors.</p>