In carbonate petroleum reservoirs, permeability impairment caused by asphaltene precipitation and deposition remains a major challenge that limits long-term productivity. This study introduces a green polymeric nanocomposite (KCl/SiO2/Xanthan/Origanum vulgare, NCs) designed to control interfacial dynamics and preserve flow capacity in carbonate formations. Using a multi-technique approach—interfacial tension (IFT) analysis, atomic force microscopy (AFM), and rock-core, fluid-flooding experiments at simulated subsurface conditions—the NCs’ abilities were evaluated in terms of their potential to modify properties at fluid–fluid and fluid–rock interfaces. The NCs increased the CO2–brine/oil IFT slope in certain pressure regions by up to 40.77%. These results indicate competitive adsorption that stabilizes interfaces. Adsorption isotherms confirmed a monolayer mechanism with a high capacity of 294.12 mg/g. AFM topographic mapping revealed order-of-magnitude changes in surface roughness (reductions in average roughness by ~75%, root-mean-square by ~83%, peak-to-valley by ~93%). These results directly link nanoscale smoothing to reduced capillary pinning. Core flooding tests demonstrated that NCs treatment decreased formation damage by up to 67.45% at 4000 psi, maintaining a high permeability ratio (k/ki = 0.87) and preserving porosity (φ/φi = 0.887, representing 88.7% porosity retention). These results establish that the studied NCs coherently manipulate fluid physics in relation to molecular adsorption and macroscopic permeability. Consequently, these NCs offer a sustainable, high-performance strategy for flow assurance and formation damage control in geological and geothermal reservoirs.