The invention discloses a method and a system for managing data of a cluster storage system and belongs to the technical field of cluster storage. The method includes that a disk file system is used for storing and managing meta data, and the data are distributed by using a catalogue as a basic unit; a client senses data distribution information and sends a data access instruction, a storage server judges whether a finding path is a root catalogue according to the data access instruction of the client, a specific active node is selected to be a target node for data access if the finding path is the root catalogue, otherwise, a Hash value is calculated according to path input parameters to obtain the data distribution information, and finding the target node for data access. According to the method and the system for managing the data of the cluster storage system, a series of relevant problems of performance bottlenecks, single point faults, data inconsistency and the like of meta data management are eliminated, system expansibility is obviously improved, and linear expansion increase of system concurrency and performances is achieved.