Porous carbonate reservoirs are characterized by strong heterogeneity and diverse pore types，with significant differences in waterflooding recovery and unclear main controlling factors. Based on the pore throat size distribution curves，the microscopic pore structure of the reservoir was qualitatively classified. Through digital core technology， a method for quantitative characterization of microscopic pore structure was established to clarify the pore throat characteristics of porous carbonate rocks in a region of the Middle Eastern，and indoor physical experiments on waterflooding were conducted to clarify the differences in the oil recovery of different types of cores and their main controlling factors. The results show that ① The microscopic pore structure of the reservoir in the study area can be classified into coarse unimodal type， fine unimodal type I， fine unimodal type II， coarse bimodal type， and multimodal type. There is no significant relationship between storage performance and core homogeneity；the single-phase flow capacity of non-unimodal type is better than that of unimodal type； unimodal type becomes worse with increasing core homogeneity.②The average coordination number and pore-throat ratio of the non-unimodal type are higher than those of the unimodal type. The average coordination number and pore-throat ratio decreased with the increase of core homogeneity for the unimodal type. The upper limit of the pore-throat ratio tends to decrease with increasing throat radius for all types，and the upper limit of coordination number increases exponentially with increasing pore radius. ③Macroscopically，core homogeneity is the main controlling factor of oil displacement efficiency； microscopically，high connectivity at large pore-throat and large pore-throat ratio at small pore-throat are the fundamental reasons for non-unimodal type to have significantly lower oil displacement efficiency than unimodal type. Porethroat size is the crucial factor of oil displacement efficiency of unimodal type.