Abstract: Regarding the extensive uncertainties result from in the probabilistic tsunami hazard analysis （PTHA）, this study summarized the sources of these uncertainties and classified their categories. The methodologies based on logic-tree and event-tree approaches were proposed to quantify uncertainties in PTHA. And then, taking the potential tsunami source （PTS） of Manila trench as an example, both methodologies were performed to illustrate their effectiveness on quantifing the uncertainties derived from the magnitude upper-limit and rupture plane parameters. Some conclusions were drawn as follows: The variability of magnitude upper-limits of PTS affects remarkably the result of PTHA, suggesting a particular consideration that could be quantified effectively using the logic-tree approach. The dip, rake and rupture areas of PTS affect moderately the result of PTHA. The guarantee rate of tsunami hazard given by PTHA will be considerably higher than 20% and slightly lower than 80% when the uncertainties are quantified by an event-tree approach, meeting the requirements of tsunami-resilient structural design.