The invention provides a safe fingerprint verification method and a system, and a safe fingerprint verification system is constructed by using an image acquisition unit, a verification characteristic extraction unit, an assisted characteristic extraction unit, a template encryption unit, a template storage unit, a registration parameter computing unit, a template decryption unit and the like. The method and the system provided by the invention take a fuzzy safety box method as a basic framework, adopt the number of ridge lines between the position of a fingerprint detailed point and the adjacent three detailed points thereof as verification characteristics, extract stable reference points from fingerprints and blocking direction fields of the peripheral specific neighborhoods thereof as assisted characteristics, use a method based on the direction field mutual information to evaluate the coincidence degree of the fingerprint registration, and search the optimum parameters by a searching strategy from roughness to refinement, namely, the optimum parameters are the registration parameter for the template fingerprint and the querying fingerprint. The registration parameters are used to convert the querying fingerprint characteristics, and encryption and verification operation are carried out on the template fingerprint by using the converted querying fingerprint verification characteristics.