The invention relates to an HBase secondary index adaptive optimization method and system. The method comprises the following steps: 1) synchronously mapping a change operation of a client on an HBaseinto an index of a distributed search engine ES through an observer coprocessor component, and maintaining an inverted index corresponding to data in the HBase by the ES to serve as a secondary indexof the HBase; 2) carrying out incremental updating on the secondary index, including incremental updating of a local index, incremental updating of a global index and incremental updating of an ES index; 3) synchronizing index updating requests of cross-table and cross-library updating HBase index tables and ES index tables to the secondary index; And 4) receiving a data query request sent by theclient, obtaining a query result through the local index, the global index and the ES index, and returning the query result to the client. The method supports multiple index modes such as a single-column index, a joint index and a full-text index, and can greatly improve the retrieval efficiency.