A method for underwater time service and synchronization and system thereof are disclosed in the present invention, in which a server can provide an accurate time benchmark and a user can perform a local time calibration by means of information interaction with the server. When a user needs to calibrate a clock, a request signal is transmitted to the server end, and the transmission time is regarded as a start point of the time service process. After receiving the signal, the server end performs a time reversal process on it to obtain a response signal, and transmits the response signal back to the user end; and transmits the accurate transmission time of the response signal to the user in manner of underwater acoustic communication. Since a time reversal mirror has the speciality for focusing time and space, the response signals are focused at the user end; the user end convolves the received signal with the original request signal to obtain a time mark signal, and accurately measures a finishing point of time service process by using the time mark signal, and the transmission time of the response signal at the server end happens to be the time's midpoint of the whole time service process. Just by using this speciality, the present invention realizes real-time time service and synchronization.