The seismic resilience of indoor substation structures is an important prerequisite for ensuring the safe service of electrical equipment inside. To clarify the seismic resilience of the substations, a finite element numerical model of a indoor substation is established. Twenty seismic waves are selected to conduct vulnerability analysis based on Incremental Dynamic Analysis (IDA). The impact of uncertainty on the vulnerability analysis of the damping structure is considered using the Latin Hypercube Sampling (LHS) method. The results show that when the structure is in the elastic stage, the dispersion of the maximum drift ratio is small. As Peak Ground Acceleration (PGA) increases, the dispersion begins to increase. With the increase in ground motion intensity, the failure probability of the substation rises sharply, and the slope of the vulnerability curve shows a trend of rapid increase followed by a gradual slowdown. When considering uncertainty, the rate of change of the median and logarithmic standard deviation of the vulnerability curve under the slight damage state LS1 is smaller than that under the severe damage state LS4. As the seismic increases, the nonlinear state of the structure amplifies the uncertainty in the vulnerability analysis, suggesting that the impact of uncertainty should be considered in practical analysis.