Based on the reflection and architectural characteristics of the high resolution seismic data, and combined with the cyclic variations of seismic attribute, the Miocene sedimentary sequence can be divided into three sequence groups and six 3rd-order sequences in the deep-water region, Southern Qiongdongnan Basin. From bottom to top, three sequence groups correspond to Sanya, Meishan and Huangliu Formations respectively. In the sequence framework, six types of typical seismic facies are indentified, which include moundy seismic facies, progradational seismic facies, channel-filled seismic facies, chaotic seismic facies, wavy seismic facies as well as parallel and sub-parallel seismic facies. Wavy reflection and parallel and sub-parallel reflection mainly develop in Sanya Formation while the moundy and wavy reflections dominates in Meishan Formation. Reefs thrived rapidly during Meishan age. Moundy and wavy reflections remained dominant but the scale of the moundy reflection was obviously minishing in Huangliu Formation compared with that in Meishan Formation. The whole Miocene sequence displayed a transgression progress in which the sedimentary environments changed from littoral and neritic to shallow marine and then gradually transited to bathyal so that fan deltas, reef shoals and channel sedimentary systems developed. It is known that the distribution and evolution of seismic facies are obviously controlled by the evolution of the sedimentary systems. It is suggested that the reefs and channel sediments may be the favorable hydrocarbon reservoirs.