Shear-wave velocity uncertainty significantly impacts seismic response analysis at engineering sites. Previous studies focused on the correlations of shear-wave velocities within soil layers. However, the influence of the vertical spatial variability of shear-wave velocity within individual soil layers was not considered. This study selected a typical Site Class II engineering site to investigate this influence based on the equivalent linear seismic response analysis method of layered soil deposits. Existing field test data on shear-wave velocity were used to discretize the shear-wave velocity within soil layers into a one-dimensional (1D) random field through covariance matrix decomposition and local average process theory. Monte Carlo simulations generated random shear-wave velocity profiles with different vertical correlation distances. Three artificial records with different earthquake return periods were used as input motions at the engineering bedrock for the 1D free-field model. Considering soil shear-wave velocity uncertainty, the peak shear strain increased by 19–27% with the input ground motion amplitude. Moreover, the site peak shear strain variability increased by 25–34% with the vertical correlation distance. The proposed 1D random field model effectively simulated the interlayer correlation and spatial variability of shear-wave velocity within soil layers, demonstrating its significance in seismic response analysis.