The invention provides a homomorphic encryption based authentication system and method for vehicular Ad-hoc networks and solves technical problems of high authentication cost and low efficiency of theprior art. The authentication method comprises the following steps: roadside unit registration implemented by a roadside unit registration request module and a trusted mechanism on a roadside unit registration response module and vehicle registration implemented by a vehicle registration request module and a trusted mechanism on a vehicle registration response module; generation of a current pseudonym of the vehicle by a V2R phase vehicle authentication request module; V2R phase authentication implemented by the V2R phase vehicle authentication request module, a V2R phase roadside unit authentication unit response module and a trusted mechanism authentication response module together; and V2V phase authentication implemented by a V2V phase vehicle authentication request module, a V2V phase roadside unit authentication response module and the trusted mechanism authentication response module together.