Molecular dynamics (MD) simulation is widely used to calculate transport properties of fluids.In this study, non-equilibrium molecular dynamics (NEMD) simulation was applied to calculate mutual diffusion coefficients from the molecular flux at a given concentration gradient. First, the applicability of spherical molecular model was investigated by calculating self-and tracer diffusion coefficients of methane and n-decane mixture by a equilibrium MD simulation. The simulated self-and tracer diffusion coefficients of both components were in good agreement with literature data except in the case that methane molar fraction was nearly equal to zero. Further, the NEMD simulation was adopted to calculate mutual diffusion coefficients of binary system of methane and n-decane. This binary system exhibits anomalous concentration dependence of mutual diffusion coefficients in the vicinity of critical molar fraction according to the previously reported experimental data. The NEMD simulation well reproduced such concentration dependence of mutual diffusion coefficients.The simulation also gave a fairly good agreement with the calculated results by the Darken equation using tracer diffusion coefficients with a thermodynamic factor.