Two isolated Neogene carbonate platforms (Xisha and Guangle carbonate platforms) have developed in the rifted uplifts since the Early Miocene. A large-scale submarine canyon system, the Zhongjian Canyon (ZJC), has developed in the tectonic depression between the two platforms since the Middle Miocene. High-resolution bathymetry data and 2D and 3D seismic data reveal the existence of the ZJC on the present seafloor, as well as in Neogene intervals. It exhibits typical characteristics of deepwater canyons that cut the surrounding rocks and indicate strong erosional features. The ZJC resulted from northwest–southeast strike-slip fault activities during synrift and postrift stages, and it periodically grew during the development of carbonate platforms since the Middle Miocene. We identified four cycles of parallel to subparallel high amplitude and dim reflectors in seismic data, which we interpreted as alternating canyon fill, based on the interpretation of seismic facies. Thus, the sedimentary evolution of the ZJC can be divided into four typical stages, which were in the Middle Miocene, Late Miocene, Early Pliocene, and Pleistocene. Considering the tectonic background of the carbonate platforms, as well as the on-going igneous activities, the sediment filling the canyon could be derived from a mixture of carbonate clasts, igneous clasts, mud, and silt. The laminar high-amplitude reflectors and dim-reflector package represented a fining-upward sedimentary cycle. The coarse-grained sediment in canyon fillings could be turbidites, carbonate debrites, and even igneous clasts. In contrast, the fine-grained sediment is likely to be dominated by pelagic to hemipelagic mud, and silt. This case study describes a deepwater canyon under a carbonate-dominated sedimentary environment and has significant implications for improving our knowledge of periplatform slope depositional processes. Furthermore, the insight gained into periplatform slope depositional processes can be applied globally.