Mishrif reservoir in the Rumaila oilfield is a typical giant reef-bank carbonate reservoir in the Middle East. Injected water breakthrough occurs easily and too early along the high permeability thin layers，thief zones，because of severe heterogeneity of reservoirs，resulting in the drop of swept efficiency of the injected water. So，the thief zone identification and the corresponding development countermeasures are the key of enhancing water flooding effect in the studied area. A method based on geological data and production performances was taken to identify thief zones. The origin of thief zones can be determined according to the core and imaging logging data. Dynamic reservoir permeability was calculated through single-well liquid production profile and other dynamic data. The thief zone can be identified after comparison of the static permeability obtained by logging interpretation and dynamic permeability. At last，development mode of the thief zone in the studied area was determined combined with sequence classification and other static data. Optimized perforation strategies of oil and water wells in various development modes of massive and layered reservoirs were put forward and applied to the flooding pilot in the Mishrif reservoir achieving expected effect after reservoir numerical simulation.