A statistical method to analyze the uncertainties of strong earthquake hazard estimation is proposed from Generalized Pareto distribution (GPD) model using the northeastern Tibetan Plateau earthquake catalogue (1885–2017) data. For magnitude threshold of 5.5, the magnitude return levels in 20, 50, 100, 200, and 500 years are 7.19, 7.70, 7.99, 8.22, and 8.45, respectively. The corresponding 95% confidence intervals are [6.77, 7.60], [7.27, 8.12], [7.53, 8.44], [7.71, 8.72], and [7.84, 9.06], respectively. The upper magnitude limit obtained from this GPD model is 9.07 and its 80% confidence interval is [8.16, 9.98]. The sensitivity analysis by the Morris method indicates that the input magnitude threshold has a relatively large influence on the estimation results. Thus, threshold selection is important for the GPD model construction. The sensitivity characteristic ranking of input factors become increasingly stable with the increasing of return period, which implies that GPD model is more suitable for estimating strong earthquakes magnitude return levels and upper magnitude limit. The GPD modeling approach and qualitative uncertainty analysis methods for strong earthquake hazard estimations proposed in this paper can be applied to seismic hazard analysis elsewhere.