The performance of MSU-S and its forms modified with phosphotungstic acid (HPW) and nickel (Ni) for the desulfurization and denitrogenation of model diesel fuel were studied. According to the results of the characteristic tests (N2 adsorption-desorption, XRD, SEM, and NH3-TPD), heteropoly acid incorporation causes higher acidity along with a negligible loss of structural aspects, while Ni impregnation leaves a drastic negative effect on mesoporous structure, crystalline phase, and particle shape along with a positive impact on surface acidity. With both modifications (HPW and Ni), the maximum increase of 33.18% and 6.88% was occurred for the adsorption loading of total sulfur and total nitrogen respectively. The adsorption loading and selectivity of all the adsorbents for total nitrogen were slightly more than those for total sulfur (the selective adsorption of nitrogen over sulfur). The pseudo-second order model can best fit the kinetics data and Freundlich model can best describe the equilibrium isotherm for all the species over Ni/HPW-MSU-S.