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The friction between a molybdenum disulphide (MoS2) nanoflake and a MoS2 substrate was analyzed using a modified Tomlinson model based on atomistic force fields. The calculations performed in the study suggest that large deformations in the substrate can induce a dramatic decrease in the friction between the nanoflake and the substrate to produce the so-called superlubricity. The coefficient of friction decreases by 1–4 orders of magnitude when a high strain exceeding 0.1 is applied. This friction reduction is strongly anisotropic. For example, the reduction is most pronounced in the compressive regime when the nanoflake slides along the zigzag crystalline direction of the substrate. In other sliding directions, the coefficient of friction will reduce to its lowest value either when a high tensile strain is applied along the zigzag direction or when a high compressive strain is applied along the armchair direction. This anisotropy is correlated with the atomic configurations of MoS2.