Surface energy (SE) is the most sensitive and fundamental parameter for governing the interfacial interactions in nanoscale carbon materials. However, on account of the complexities involved of hybridization states and surface bonds, achieved SE values are often less in comparison with their theoretical counterparts and strongly influenced by stability aspects. Here, an advanced facing-target pulsed dc unbalanced magnetron-sputtering process is presented for the synthesis of undoped and H/N-doped nanocrystalline carbon thin films. The time-dependent surface properties of the undoped and H/N-doped nanocrystalline carbon thin films are systematically studied. The advanced plasma process induced the dominant deposition of high-energy neutral carbon species, consequently controlling the intercolumnar spacing of nanodomain morphology and surface anisotropy of electron density. As a result, significantly higher SE values (maximum = 79.24 mJ/m2) are achieved, with a possible window of 79.24-66.5 mJ/m2 by controlling the experimental conditions. The intrinsic (size effects and functionality) and extrinsic factors (atmospheric exposure) are resolved and explained on the basis of size-dependent cohesive energy model and long-range van der Waals interactions between hydrocarbon molecules and the carbon surface. The findings anticipate the enhanced functionality of nanocrystalline carbon thin films in terms of selectivity, sensitivity, and stability.