Abstract: The Cenozoic Beibuwan Basin is located in the southwest margin of the South China Block. Many depositional breaks and unconformities have been found in the Cenozoic sequence. The characteristics and distribution pattern of these conformities are described in details in this paper. According to their scale and behaviors, these unconformities can be divided into three orders. And based on ages and their relationship with the rifting stages of the basin, there are three main types of unconformities, i.e. rifting phase unconformity, rifting-depression phase unconformity and inversion phase angular unconformity. The basal unconformity of the basin recorded the initial rifting event of the basin. Being the first-order unconformity, it formed in the rifting phase, and was in conjunction with the sudden decrease in the subduction rate of the Pacific Plate. The unconformity beneath the Weizhou Formation was interpreted in this paper as a rifting phase third-order unconformity formed by the Zhuqiong Movement. It is regionally associated with the collision of the Indian Plate to the Eurasian Plate and the turn of the subduction direction of the Pacific Plate. The unconformity at the bottom of the Xiayang Formation is the transitional interface of the basin structural systes. As a second-order unconformity, it corresponds to the continuous opening of the South China Sea Basin. The unconformity at the bottom of the Dengloujiao Formation is considered as the result of the tectonic inversion of the basin in the later stage. It is a third-order angular unconformity formed in the inversion phase. From a regional point of view, it is related to the Indian-Australian Plate, rather than the subduction of the Philippine Sea Basin. It is concluded that the formation of unconformities is closely related to the rifting of the South China continental margin and the multiple-order and multiple-phase transtension or transpression. It is believed that the intensively strike-slip faulting along the South China continental margin is the result from the reorganization of the regional plate tectonic pattern.