Diamond‐like carbon (DLC) films are capable of achieving superlubricity at sliding interfaces by a rapid running‐in process. However, fundamental mechanisms governing the friction evolution during this running‐in processes remain elusive especially at the nanoscale, which hinders strategic tailoring of tribosystems for minimizing friction and wear. Here, it is revealed that the running‐in governing superlubricity of DLC demonstrates two sub‐stages in single‐asperity nanocontacts. The first stage, mechanical removal of a thin oxide layer, is described quantitatively by a stress‐activated Arrhenius model. In the second stage, a large friction decrease occurs due to a structural ordering transformation, with the kinetics well described by the Johnson–Mehl–Avrami–Kolmogorov model with a modified load dependence of the activation energy. The direct observation of a graphitic‐layered transfer film formation together with the measured Avrami exponent reveal the primary mechanism of the ordering transformation. The findings provide fundamental insights into friction evolution mechanisms, and design criteria for superlubricity.