The variations in seismic response between deep soft soil sites with different shear wave velocities were not fully understood. This study focuses on the seismic response of deep soft soil sites in the lower reaches of the Yangtze River, China. A nonlinear dynamic finite element model was developed for two representative deep soft soil sites with borehole profiles and the shear wave velocity tested by the single borehole method. Two nonlinear cyclic constitutive models are used and thus compared through the site seismic response. To accurately calibrate the nonlinear cyclic model parameters, resonant column tests were conducted on 21 soil samples collected from the two boreholes. The results show that the peak ground acceleration (PGA) under low-frequency (Liuan) input motion was higher for soft soil sites compared to that under medium- and high-frequency (Kobe and Nahanni) input motions. The PGA amplification factor for deep soft soil sites under different input motions can be approximated by an exponential function. The peak ground acceleration tends to be lower as the equivalent shear wave velocity (Vse) decreases. The shapes of the spectral acceleration were similar for the two sites, despite a substantial difference in the Vse between them. Additionally, a crossover point was observed in the spectral acceleration for the two sites. The period corresponding to this crossover point increased with increasing intensity of input motions, indicating that the sites became softer with higher intensity and thus generally exhibited a longer characteristic period of the spectral acceleration. This paper also highlights the significance of selecting nonlinear constitutive models and the precise calibration of model parameters in the seismic response analysis of deep soft soil sites, providing a scientific basis for future similar site analyses.