To evaluate seismic risk and identify critical pipelines of water supply system, water supply index(S), pipeline update profit(U) and pipeline break consequence(B) are set up to describe system seismic performance, and the graphical iterative response analysis of flow following earthquakes (GIRAFFE) based on Monte Carlo simulation is applied to the hypothetical water supply system for peak ground velocity vG=50 cm/s. The simulation result shows that the distribution of S is related to nodes’ demand pattern in the system. Calculated by running single Monte Carlo simulation, U could be used as primary indicator to identify individual critical pipelines and maximum benefit portfolio, and it is the consequence of B and pipelines’ damage probability. Updating the group with largest individual critical pipelines is not the best strategy for the system,and the system seismic performance would be most improved by updating maximum benefit portfolio.