A method and system for service clock transparent transmission in an optical transport network (OTN) are provided. The system includes a service accessing end and an OTN receiving end; the method includes the following steps: the OTN receiving end performs de-mapping operation to an OTN frame after receiving the OTN frame, and performs two-level buffering operation to the service data flow recovered therefrom, a first buffering unit performs a homogenization treatment to the service data flow and then outputs to a second buffering unit, which the second buffering unit outputs the service data flow according to the service clock after receiving the service data flow. After adopting the present invention, it is able to ensure that the quality of the recovered service clock is relatively higher, which meets the customer requirement on the related specification of the service clock.