This study aimed to clarify the effect of a unique structure with a “shoulder,” which represents a hump on the high wave vector side of the first peak of static structure factor, in liquid Sn (liq-Sn) on the self-diffusion behavior through molecular dynamics (MD) simulation. The MD simulations of liq-Sn at 573 K and liquid Pb (liq-Pb) at 773 K were performed for comparison. The former and latter were selected as element with and without shoulder structure and reliable self-diffusion coefficients in liquid have been measured in both elements. The calculated self-diffusion coefficients of liq-Sn and liq-Pb were reproduced as the same order of magnitude with the referred reliable data of diffusion coefficients, which were obtained by experiments on the ground. The microscopic diffusion behavior of liq-Sn is unlike that of the hard-sphere model because the atoms become sluggish in the range that corresponds to the shoulder appearing in the pair distribution function of liq-Sn as well as in the structure factor of liq-Sn based on the local atomic configurations and time-series analyses of individual atoms. Therefore, the velocity autocorrelation function (VACF) converges to zero more rapidly than that of liq-Pb, and it is reproduced by the hard-sphere model. However, the macroscopic diffusion behavior of liq-Sn expressed by the self-diffusion coefficient is the same as that of the hard-sphere model with the non-correlation of the VACF in the long time.