Detonation nanodiamonds (DNDs) are known to be produced in aggregated clusters of a few nanometer-sized primary crystalline particles embedded in an amorphous carbon matrix exhibiting high degree of polydispersity. A commonly accepted mechanism behind DND aggregation is the bridging of primary particles via oxygen containing functionalities. Here, we provide definitive spectroscopic evidence in favor of this working mechanism by carrying out systematic chemical compositional analysis on monodispersed DND aggregates of various sizes. Oxygen content is found to increase proportionally with the aggregate size confirming the role of oxygen containing functionalities as a cross-linker. Solid-state nuclear magnetic resonance data confirms these linkers to be of ether (COC) nature. Our results imply that oxygen content in DNDs can be independently tuned by varying the aggregate size, a knowledge which might benefit other applications, in addition. Next, we use this understanding to engineer the DND surfaces via an acid hydrolysis step to strip off these oxygen functionalities leading to size reduction of ca. 150 nm as-received DND aggregates to ca. 40 nm with >90% yields, without resorting to any other pre- or post-hydrolysis treatment such as surface functionalization or milling.