Maintaining wellbore stability in deep and ultra-deep formations demands plugging agents capable of sealing nano- to micro-scale pores under high-temperature conditions. A core–shell nano-plugging agent (CSP) was synthesized via emulsion polymerization using KH-570-modified nano-SiO₂ as the rigid core and a poly(styrene-co-butyl acrylate-co-methyl methacrylate) terpolymer as the deformable shell. CSP particles had a mean diameter of 196.5 nm (polydispersity index, PDI = 0.183) and an onset decomposition temperature of 342 °C. Compatibility tests at 180 °C confirmed that 3 wt% CSP caused no adverse changes in the rheology or emulsion stability of the oil-based drilling fluid (OBM). At 180 °C, CSP reduced the high-temperature high-pressure (HTHP) filtrate loss by 64.4% and the permeability plugging apparatus (PPA) filtrate loss by 66.1%. Sand-disk tests elevated the breakthrough pressure from 1.5 to 9.2 MPa. Core displacement on sandstone cores achieved a plugging rate of 98.30%, and pressure transmission tests on natural shale cores extended the 50% equalization time by 7.8-fold. Comparative evaluation confirmed that the core–shell architecture consistently outperformed nano-SiO₂ alone, polymer alone, and their physical blend. Low-temperature N₂ adsorption provided direct evidence of pore sealing, with the treated-shale Brunauer–Emmett–Teller (BET) surface area and total pore volume reduced by about 62% (12.6 to 4.8 m²/g and 0.0325 to 0.0121 cm³/g, respectively). Scanning electron microscopy of the shale surface before and after treatment further provided direct visual evidence of pore sealing, showing the open, porous matrix being converted into a dense, compacted filter cake. Filter-cake thickness measurements are consistent with a proposed three-stage plugging mechanism—bridging, deformation filling, and thermal compaction—driven by the complementary roles of the rigid core and the deformable shell. These findings indicate that CSP merits further evaluation as a high-temperature plugging agent for wellbore stabilization in deep shale formations.