The invention provides a domain-based file encryption protection method, mainly for solving the safety problems in an electronic document sharing, storing and propagation process in a domain. The invention brings forward a domain-based electronic document encryption method for the purpose of overcoming the defects in the prior art of document protection. All secret electronic documents in the domain are encrypted so as to realize secret document encryption storage, transparent transfer of the secret documents in the domain, and copying of the secret documents out of the domain or loading to the internet, the secret documents being not able to be parsed.