In deep oil reservoir development, enhanced oil recovery (EOR) techniques encounter significant challenges under high-temperature and high-salinity conditions. Traditional profile-control agents often fail to maintain stable blocking under extreme conditions and exhibit poor resistance to high temperature and high salinity. This study develops a functionalized nanographite system (the MEGO system) with superior high-temperature dispersibility and thermosalinity-responsive capability through polyether amine (PEA) grafting and noncovalent interactions with disodium naphthalene sulfonate (DNS) molecules. The grafted PEA and DNS provide steric hindrance and electrostatic repulsion, enhancing thermal and salinity resistance. After ten days of aggregation, the MEGO system forms stable particle aggregates (55.51–61.80 µm) that are suitable for deep reservoir migration and profile control. Both experiments and simulations reveal that particle size variations are synergistically controlled by temperature and salt ions (Na⁺, Ca²⁺, and Mg²⁺). Compared with monovalent ions, divalent ions promote nanographite aggregation more strongly through double-layer compression and bridging effects. In core displacement experiments, the MEGO system demonstrated superior performance in reservoirs with permeabilities ranging from 21.6 to 103 mD. The aggregates formed within the pore throats significantly enhanced flow resistance, expanded the sweep volume, and increased the overall oil recovery to 56.01%. This research indicates that the MEGO system holds excellent potential for EOR in deep oil reservoirs.