The invention provides a method and a system for analyzing a fault root cause. The method comprises the following steps that: according to the time attribute of each piece of data in a dataset, carrying out sorting, and segmenting the dataset according to a preset time window to obtain multiple groups of sub-datasets; according to an Apriori algorithm, obtaining a frequent item set and an association rule in the dataset, wherein the frequent item set contains a certain quantity of data with a strong association relationship; and according to the time attributes of the data in the frequent itemset, carrying out sorting, matching the data which ranks higher with adjoint warning cause data pre-stored in a warning cause database in sequence, if the data which ranks higher is successfully matched with the adjoint warning cause data pre-stored in the warning cause database, removing the data which ranks higher from the dataset, and continuously carrying out comparison from a next data itemuntil the data which fails to be matched and ranks higher is taken as the root cause of the data of which the time sequence ranks at the bottom in the frequent item set. The method is suitable for thefull-dimension monitoring scene of an IT (Information Technology) system, the pressure of operation and maintenance personnel is released, and the quality requirements of the operation and maintenance personnel are lowered.