Volatiles in small bodies provide important clues to solar system evolution and are of in-situ-resource-utilization interest. Explicit modeling of small bodies’ global thermophysical process is essential to assess volatiles’ evolution and abundance. Previous numerical studies commonly use a finite difference/volume method, which has limited capability in simulating the interior thermal dynamics of small bodies with realistic shapes. Here we developed a novel 3D framework using the generalized finite difference method for modeling thermal evolution of active small bodies (GTasb3D). By fully solving the energy and mass conservation equations using a mesh-free, Cartesian-coordinate-based method, this framework can evaluate the heat and mass transport in a porous cometary body of various shapes. Several tests and comparisons with previous studies have been carried out to verify this framework's accuracy and efficiency. We show that the timescale to achieve thermal equilibrium and the global temperature distribution are in good agreement with previous theoretical and numerical estimates. The GTasb3D simulations show that ice sublimation mainly occurs near the ice front, and parts of the resulting vapor recondense beneath the ice front. The surface gas density dramatically decreases as the ice retreats. For a 1 km radius object located at 3 au with initially homogeneous dust-ice distribution, the depth to ice at the equator is >∼2 cm after ∼10 yr, assuming that a dust mantle is left behind after ice depletion. At this stage, the global gas production rate is below the gas emission detection capability but is capable of lifting submillimeter-sized dust from the nucleus’s near-subsurface.