Abstract: The Okinawa Trough is a typical back-arc basin of the west Pacific arc-basin system resulted from the joint action of the Pacific plate, Eurasian plate and Philippine Sea plate. It is located in the Pacific activation zone since Miocene. Owing to the seafloor spreading, there occur high heat flow values and active volcanic activities in the trough. Sediments are coming from marine biogenic materials and terrigenous debris, which contains rich formation of the paleo-environment and the climate change. Therefore, the study of high resolution sequence stratigraphy and sedimentation rate is critical important. In this paper, the high resolution sequence stratigraphy of the trough is established based on the wavelet transform and logging curve interpretation. Milankovitch and astronomical cycle are used for spectrum analysis. Sedimentation rate and the duration are calculated, in addition to tuning logging and astronomical cycle curves. Finally, a sequence on astronomical scale with accurate time is established.