The method of secure communication between the endpoints is used for the secret communication between endpoints locating in different gatekeeper management area, and the method includes: in the process of the caller endpoint calling the callee endpoint, the home gatekeeper of the callee endpoint generates the share secret key between the caller endpoint and the callee endpoint; the secure communication process is performed between the caller endpoint and the callee endpoint according to the share secret key. According to the secure communication method between the endpoints, the invention makes that secret communication mechanism between the endpoints locating the different gatekeeper management area has better expansibility and higher efficiency.