Based on the analysis of geological characteristics of ultra-deep fault-controlled fracture-cavity carbonate reservoirs and division of reservoir units, two physical models were made, and physical simulations of oil displacement by water injection were carried out to find out water flooding mechanism in the fault-controlled fracture-cavity carbonate reservoir under complex flow state. On this basis, a mathematical model of fault-controlled carbonate reservoir with coexisting seepage and free flow has been established. Pilot water injection tests have been carried out to evaluate the effects of enhancing oil recovery by water injection. The results show that: fault-controlled fracture-cavity carbonate reservoir units can be divided into three types: the strong natural energy connected type, the weak natural energy connected type and the weak natural energy isolated type; the fault-fracture activity index of the fault-controlled fractured-cavity body can effectively characterize the connectivity of the reservoir and predict the effective direction of water injection; the mathematical model of fault-controlled carbonate reservoir with coexisting seepage and free flows can quantitatively describe the fluid flow law in the fracture-cavity body; the water injected into the fault-controlled fracture-cavity body is weakly affected by the capillary force of the lithologic body, and the oil-water movement is mainly dominated by gravity. The development modes of single well water injection, unit water injection, and single well high pressure water injection proposed based on the connection structure of fracture- cavity space and well storage space configuration are confirmed effective by pilot tests, with obvious water injection gravity flooding effect.