The present disclosure provides a security authentication method, system and device for IoV communication based on a national cryptographic algorithm. The method of the present disclosure includes: constructing, by an on-board unit, an identity authentication request message for transmitting to a road side unit; receiving, by the on-board unit, an identity authentication response message, and verifying a signature; and if the verification is successful, calculating, by the on-board unit, a session key and a hash value thereof, and constructing an acknowledgment message for transmitting to the road side unit, where the acknowledgment message is used in calculating a session key and a hash value thereof by the road side unit for contrast verification; if hash values are equal, security authentication is successful and a session key is generated; and if the hash values are not equal, the security authentication is failed.