The invention discloses a fast statistical query method for mass medical data. The method includes: firstly, collecting, filtering and processing medical data from different data sources, and storing processed medical data into an HDFS (Hadoop distributed file system) or HBase; using the HDFS or HBase to create and initialize statistics trees for one or certain statistics-based medical data; subjecting the newly added medical data to single or multiple incremental computations, and updating the statistics tree by results of the incremental computations; allowing a server to respond to a statistical query request from a user according to the one or a plurality of created statistics trees, to analyze the statistical query request into sub-queries based on one or the plurality of statistics trees, and to combine into a plurality of sub-query results fed back to the user. The position of statistical data can be located quickly by the method, access to mass data is avoided, system load is lightened, and query efficiency and access concurrency are increased.