Intraflagellar transport (IFT) is a core mechanism for ciliary assembly, length maintenance, ciliary proteome homeostasis and signal transduction. Most proteins required for ciliary structure and function are synthesized in the cytoplasm. Because the ciliary compartment is separated from the cell body by the selective barrier of the transition zone, these proteins cannot freely equilibrate between the cytoplasm and the cilium. Consequently, axonemal components, membrane proteins and signaling molecules must be actively imported into cilia, retrieved from the ciliary compartment, and recycled or degraded through highly ordered transport and sorting pathways. The IFT system is mainly composed of the IFT-A complex, IFT-B complex, kinesin-2, dynein-2 and the Bardet-Biedl syndrome protein complex (BBSome). Through coordinated anterograde and retrograde transport, these modules mediate the dynamic trafficking of different classes of ciliary cargoes. Anterograde transport delivers structural and membrane-associated components from the ciliary base toward the ciliary tip, whereas retrograde transport retrieves IFT components and selected cargoes back toward the ciliary base and cytoplasm. In this way, IFT not only supports the construction of the axoneme but also contributes to the maintenance of ciliary composition and the regulation of ciliary signaling activity. In recent years, advances in cryo-electron microscopy, in situ cryo-electron tomography and single-molecule imaging have greatly improved our understanding of the molecular mechanisms underlying IFT. These approaches have revealed how IFT trains are assembled at the ciliary base, how they move along axonemal microtubule tracks, how they undergo directional switching at the ciliary tip, and how cargoes are retrieved and recycled. Among the IFT modules, IFT-B acts as the major scaffold of IFT trains. It participates in cargo loading, motor coupling and initiation of anterograde transport. IFT-A is involved in retrograde transport, membrane protein adaptor function and train remodeling. The BBSome, through reversible association with the IFT system, regulates ciliary membrane protein sorting, signaling receptor clearance and renewal of the ciliary proteome. These functions indicate that the IFT machinery is not a simple linear transport pathway, but rather a dynamic and reconfigurable transport system. The conversion of transport direction is a key step in the IFT cycle. This process is closely associated with disassembly of anterograde trains, dissociation of kinesin-2, activation of dynein-2 at the ciliary tip and reassembly of retrograde trains. In terms of pathogenic mechanisms, IFT abnormalities may cause ciliopathies through four major pathways: defects in ciliary assembly and structure, abnormal localization of ciliary cargoes, dysregulation of signaling pathways, and impaired cargo unloading and retrieval. These defects can affect multiple organ systems, including the retina, kidney, skeleton, respiratory tract, reproductive system, and neuro-metabolic system. Current therapeutic strategies are still mainly based on symptomatic support and maintenance of organ function. Overall, IFT is a dynamic transport system jointly regulated by axonemal structure, motor activity, cargo selection and cellular signaling. It links ciliary architecture with protein turnover and signaling regulation, thereby playing a fundamental role in both ciliary homeostasis and ciliopathy pathogenesis. Further elucidation of IFT regulatory mechanisms and their relationships with disease phenotypes will help promote mechanism-based classification, genetic diagnosis and precision intervention for ciliopathies.