The invention relates to a data storage system and a data storage method of large data. The system comprises a four-layer structure. The metadata structure layer defines and stores a plurality of metadata types and attributes of the metadata types. The metadata layer defines and stores all the association relations between metadata object information and metadata object according to the attributesof metadata type. The data structure layer defines and stores the structural relationship of statistical data according to the metadata object information. The data layer stores statistical data according to the structural relationship of the statistical data. The invention is based on DDI metadata standard, Defines a four-tier structure for statistical data storage: metadata structure, Metadata,data structure and data, so as to unify the storage and management of massive micro-data according to the big data structure, break down the barriers of data resource integration, realize the flexible and efficient storage and use of statistical data, and then largely solve the problems of large amount of data, complex structure, rapid growth rate, and data analysis and use difficulties and so on.