The invention relates to a fingerprint eigenvalue encryption-decryption system which comprises a fingerprint sensor, a nonvolatile store and a fingerprint encryption-decryption chip. The fingerprint encryption-decryption chip comprises a special interface of the fingerprint sensor, a fingerprint matching module, a fingerprint eigenvalue extracting module, a special channel of the fingerprint matching and the fingerprint eigenvalue extracting, a bus interface of the fingerprint eigenvalue extracting module, a fingerprint comparing module, a bus interface of the fingerprint comparing module, an interface of the nonvolatile store, a controller, a bus interface of the controller, a communication port, an internal bus. The fingerprint encryption-decryption chip also comprises an encryption-decryption module, a one time programmable program store, a bus interface of the encryption-decryption module and a bus interface of the one time programmable program store. The invention can improve the safety of the fingerprint eigenvalue and enhancing the safety level. The integration of the fingerprint eigenvalue extracting, the fingerprint comparing and the encryption-decryption reduces the cost of the system; the system solves the safety problem of remote transmission of the fingerprint eigenvalue, thus leading a fingerprint database to be easily centralized and conveniently managed and searched.