Because of the characteristics of transient electromagnetic disturbance characteristics like small sample and large dispersion, and combined with Bootstrap method, a bias-corrected bootstrap confidence interval estimation method and the B-type uncertainty evaluation method for multiple measurements are proposed. First, the transient electromagnetic disturbance of the secondary cable port during a switching operation is measured in the substation. Then, a random weighting method based on the Bootstrap and a self-confidence interval estimation method for deviation correction are applied to obtain the statistical mean and confidence interval of the characteristic parameters. Then the B-type uncertainty evaluation method for multiple measurements is applied to obtain the uncertainty of the characteristic parameters. Finally, the compliance between the standard waveform characteristic parameters and the measured waveform is evaluated. The results show that the dispersion of the peak-to-peak disturbance voltage from multiple measurements is the major factor in the uncertainty; the rise time of the measured disturbance voltage in the 100~300 kHz range is significantly longer than that of the 100 kHz slow damping oscillation wave; the rise time of the measured disturbance voltage in the 6.5~10 MHz range is significantly longer than that of the fast damping oscillating wave; the duration of measured disturbance voltage waveform decreases with increasing frequency of the interval.