The development of anti-rhythmic carbonate reservoirs in the Middle East often encounters challenges such as water hold-up and reverse coning during the water injection process, leading to premature water breakthrough and various water-out issues. The unclear understanding of these phenomena, attributed to strong reservoir heterogeneity, results in a relatively low recovery degree in water injection development. This paper investigates the mechanisms behind water hold-up and reverse coning phenomena, offering detailed solutions. Numerical models of the oil reservoirs were developed, and an extensive study of influencing factors, including reservoir types, Kv/Kh, water injection pressure differential, wettability, and perforation position, was conducted to unveil the underlying mechanisms. Key findings indicate that the water hold-up phenomenon is influenced by capillary force barriers due to wettability and high-perm streaks, while the reverse coning phenomenon depends on the combined forces of gravity, capillary force and downward production differential among which downward production differential is the dominant factor compared to capillary force and gravity. The study also proposes a differential perforation principle tailored to different water-out types to enhance vertical sweep efficiency. The differential perforation principle is as follows: the optimal perforation position is at top layer and the optimal perforation length approximately accounts for 1/4 of the total oil layer thickness for water-out in bottom; the avoidance perforation height in top accounts for 1/6 of the total oil layer thickness and the optimal perforation length approximately accounts for 1/2 of the total oil layer thickness for water-out in top; the avoidance perforation height in top and bottom accounts for 1/5 and 2/5 of the total oil layer thickness respectively for water-out in both top and bottom.