Synchronal comminution via high-energy bead milling not only efficiently pulverizes Si particles and exfoliates graphene oxide (GO) sheets but also facilitates Si surface functionalization and intensify Si-C conjugation. After a thermal reduction, a well-wrapped Si@C anode material can be fabricated for lithium storage. The discharge specific capacities of this Si@C composite sustain at 1110.3 mAh g−1 after 300 cycles at 1 A g−1 and 316.4 mAh g−1 for 800 cycles at 5 A g−1, which are respectively 1.35 and 2.07 times that of its random blended Si/C counterpart. By employing molecular dynamics (MD) simulations with ReaxFF reactive force field to investigate the mechanochemical reactions between Si and GO amidst high-energy milling, an atomic scale portrayal of Si crystal fragmentation and Si-C bonding can be depicted. Analyses focusing on the differential forces exerted on various Si crystal planes, coupled with potential energy (PE) trends, reveal a higher propensity for cleavage in (111) plane, with (311) plane followed. Radial distribution function (RDF) outcomes indicate that ball milling leads to substantial disruption of crystalline order in Si particles, generating a plethora of Si dangling bonds. This disruption stimulates the formation of SiOOC, SiOC and SiC bonds at the Si/C interface, thus enhancing the integration of GO with Si substrate. Subsequent thermal reduction processes not only restore the structural order of Si and GO but also consolidate Si/C bonding.