Abstract: Considering the strong coupling effect due to the continuous flow of fuel pebbles in the core, the uncertainty analysis framework and tool of the light water reactor are not immedieatly applicable to the pebble bed high-temperature gas-cooled reactor (PB-HTR), and it requires special treatment due to the characteristics related to the pebble bed. Based on design and engineering experience of PB-HTR, Institute of Nuclear and New Energy Technology (INET) of Tsinghua University performed in-depth study on uncertainty analysis of HTR and has achieved some progresses in recent years. The framework of uncertainty analysis for PB-HTR has been established and the uncertainty analysis tool VSOP-UAM has been developed based on the HTR reactor physics code VSOP. VSOP-UAM has the capability of describing the realistic operation characteristics of the pebble bed core, and conducting the complete analysis of the implicit effect and the explicit effect of nuclear data uncertainty. SCALE/TSUNAMI-3D and VSOP-UAM codes were used to model the fuel pebble, the core unit, the initial state and the equilbrium state of the core, and the propagations of the uncertainty of the nuclear data to the system parameters were quantified. Additionally, the effects on effective multiplication factor (k_eff) and the power distribution of the core from the mixture of pebble flow, the uncertainty of filling fraction of the pebble bed and the uranium loading in fuel pebble, were also quantified and assessed. Some valuable observations were made through the analysis, which are different from the light water reactor results.