Earthquake effects of two typical deep soft sites selected from Tianjin(site 1)and Shanghai(site 2) are studied when the vertical inputting earthquake waves are located in different depth of sites. As far as the shear wave velocity of soil layers is concerned, seven kinds of soil layers in site 1 and eight soil layers in site 2 are selected as the vertical imputing interfaces of earthquake waves. Two acceleration waves recorded during Taft earthquake and Northbridge earthquake are selected, and the peak values of two waves are adjusted to be 0.35m/s2、0 70m /s2 and 0 98m /s2, respectively. The earthquake response of sites is calculated by SHAKE91 program. The results are compared to those of site when the input interfaces of earthquake waves are located in bedrock with shear wave velocity larger than 500m/s. The conclusion is as following: With the depth of input position (or shear wave velocity) increasing, the value of the ground acceleration response spectrum gradually closes to the actual data.; For the general building the soil layer with shear wave velocity for 400m/s or so can be chosen as the input interface, and the building with long natural vibration period should be treated seriously, and the soil layer whose shear wave velocity is above 500m/s can be chosen as the input interface.