The invention discloses a method and a system for the smooth registration of a transport stream. The method comprises the following step of: during the insertion or interception of the transport stream, inserting one or more transport packets carrying a time synchronous reference and timestamps at a registration point, or inserting the clock synchronization reference into a first subsequent transport packet at the registration point. By the method and the system, in a program insertion process or a program edition process, the clock synchronization reference of a program is calculated and updated, so that a subsequent program can quickly acquire the clock synchronization reference after the insertion or edition of the program is finished.