The invention is used for fingerprint indexing of an ultra-large type fingerprint database. The invention discloses an indexing structure and retrieval method for an ultra-large type fingerprint database, belongs to the computer identification field, and in particular relates to the fields such as fingerprint identification, database, data retrieval, image processing, etc. The invention disclosesa construction method for an ultra-large type fingerprint database retrieval system structure, an index evaluation method based on index matching error probability, a fingerprint indexing method based on layering depth index, and an index evaluation method based on one-edge and multiple-time matching structure characteristics for quickening the indexing of the ultra-large type fingerprint database, which have practical value and common applicability. In the off-line database establishment procedure, three searchers with complementary functions of hash indexing, layering depth indexing and characteristic value indexing are built according to the index evaluation method based on index matching error probability; and in the on-line indexing procedure, searchers according to the index evaluation method based on index matching error probability and the index evaluation method based on one-edge and multiple-time matching structure characteristics are built.