A soft site in the coastal area of Tianjin is used for analysis as an example of the seismic response of a site with horizontally-layered soil. The ground motion time history with different intensities and phases was input, and the equivalent linearization method was used to consider the nonlinear dynamic characteristics of the soil. This study also presents the effects of a relation between variability in the curves of dynamic parameters of a thick layer of mucky silty clay in the Tianjin area (including the soil dynamic shear modulus ratio and damping ratio) on the peak value of ground surface acceleration and its response spectra in deep soft sites. Numerical results obtained from a number of case studies were used to make a comparison with a standard condition, and the following was determined. Firstly, adding or reducing one standard deviation to the mean of the damping ratio has little effect on ground motion parameters. Secondly, addition or reduction of one standard deviation to the mean value of the dynamic shear modulus ratio has a prominent effect on the peak value of ground surface acceleration; when the ground motion time history input is 2% of the 50 years transcendental probability the corresponding peak value of ground surface acceleration increases or decreases by 20% to 30%, and the surface response spectra is changed into a thin-high or short-fat trend. Thirdly, the mean value of the dynamic shear modulus ratio when one standard deviation is added, has a significant effect on the peak value of ground surface acceleration for 10% of the 50 year exceedance probability, the corresponding peak value of the ground surface ratio decreases by about 15% and the response spectra is changed into a short fat trend. Finally, when one standard deviation is added or subtracted from the mean value of the dynamic shear modulus ratio or damping ratio there is little effect on the value of ground motion parameters.