A large-rimmed carbonate platform was developed in the Amu Darya Basin during the Middle-Late Jurassic Callovian-Oxfordian period. What distinguishes it from typical carbonate platforms is that a series of reef-bank complexes had extensively developed in the deep shelf depositional zone of the basin. However, only a few studies have reported on the classification, characteristics, and genesis of these reef-bank complexes in relatively deep water, greatly limiting the development of deep-water carbonate sedimentology. To address this issue, the types and the genesis of reef-bank complexes in the deep shelf environment have been clarified based on the systematic petrography, seismic sedimentology, and geomorphology study of the Callovian-Oxfordian carbonate rocks in the northern Amu Darya Basin during the Middle-Late Jurassic period. The results find that the reef-bank complexes are widely distributed in the deep shelf environment in the study area with laminar, reticulated, and zonal distributions. The reef-bank complexes include barrier-bonding reef-bank complexes, lime-mud mounds (LMMs), and granular shoals (GSs). The deep shelf environment can be further divided into an inner shelf, shelf margin, and shelf slope. The inner shelf and shelf margin have a relatively shallow water body and a strong sedimentary hydrodynamic force, mainly developing reticulated reef-bank complexes and laminar GSs, whereas the shelf slope mostly develops zonal LMM deposits in strips. The scale of the reef-bank complexes is mainly controlled by basement paleogeomorphology and water energy. Relatively high-energy reef-bank complex bodies are developed on the seaward side of the paleouplift limb with relatively turbulent hydrodynamic conditions, whereas low-energy LMMs are mostly developed on the high position of paleouplift and landward side. The obtained findings can deepen our understanding of relatively deep-water carbonate sedimentation and enrich the carbonate sedimentation theory.