The invention discloses a HBase secondary index system based on Elastcisearch. The system comprises a data table design module, a key-value matching module, a row key return module, a multi-table joint query module, a standard SQL query module and an interface module. It includes designing secondary index based on distributed column database, establishing index system for column value of distributed column database by secondary index technology, and creating index table automatically and efficiently by co-processor technology, which can break the defect of HBase lacking column family index. Supports the dynamic increase or decrease of index, reduces the network overhead caused by random query, and improves the scalability and practicability of secondary index. Aiming at the problem of weakSQL operation ability of distributed data storage, SQL parser and executor are designed and parallel SQL query engine is constructed. SQL operation is transformed into Region scan operation by usingdistributed column database API, coprocessor and filter, and efficient parallel SQL query is realized by making full use of two-level index mechanism.