In window-based Internet service fault management,improper time window size setting will affect the fault diagnosis algorithm. In order to reduce the impact,challenges of Internet service fault management are analyzed in this paper,and a layering model is recommended. Bipartite graph is chosen to be the fault propagation model (FPM) for each layer. A window-based fault diagnosis algorithm MFD (multi-window fault diagnosis) is proposed for the bipartite FPM. MFD takes the correlation of adjacent time windows into account. As a result,it can reduce the impact of improper time window size setting. Simulation results prove the validity and efficiency of MFD.