This study is devoted to estimate higher-mode effects for multi-story structures with considering soil-structure interaction subjected to decomposed parts of near-fault ground motions. The soil beneath the super-structure is simulated based on the Cone model concept. Two-dimensional structural models of 5, 15, and 25-story shear buildings are idealized by using nonlinear stick models. The ratio of base shears for the soil-MDOF structure system to those obtained from the equivalent soil-SDOF structure system is selected as an estimator to quantify the higher-mode effects. The results demonstrate that the trend of higher-mode effects is regular for pulse component and has a descending variation with respect to the pulse period, whereas an erratic pattern is obtained for high-frequency component. Moreover, the effect of pulse component on higher modes is more significant than high-frequency part for very short-period pulses and as the pulse period increases this phenomenon becomes vice-versa. SSI mechanism increases the higher-mode effects for both pulse and high-frequency components and slenderizing the super-structure amplifies such effects. Furthermore, for low story ductility ranges, increasing nonlinearity level leads to intensify the higher-mode effects; however, for high story ductility, such effects mitigates.