Prior research demonstrated that the uncertainty of soil parameter can significantly impact the seismic response analysis and seismic performance evaluation of underground structures. To this end, the seismic response of a three-story, three-span subway station embedded in a typical layered engineering site was investigated in this study and the uncertainty of soil parameters was explicitly considered using the shear-wave velocity interlayer correlation model. In addition, an incremental dynamic analysis considering the uncertainty of the shear-wave velocity was performed using the one-dimensional convolutional neural network (1D-CNN) model as a surrogate model for the traditional finite element method. The results indicate that the uncertainty of soil shear-wave velocity increases the average PGA values for minor, moderate, and severe failures with a probability of exceeding 50% by about 10%, and increases the logarithmic standard deviation by about 40%. When considering the uncertainty of shear-wave velocity, the discreteness of the fragility curve will increase. Moreover, the rightward shift of the fragility curve midpoint leads to a comparatively more safety seismic performance evaluation of the structure under significant seismic input.