Fracture-vuggy carbonate reservoirs commonly exhibit sufficient bottom water energy and are characterized by fractures or other interconnected channels with bottom water, which can easily cause high water cut in oil wells during production. The main reasons are as follows: firstly, bottom water coning leads to water flooding. Secondly, artificial water injection flooding fails and shows high water cut in oil production. This paper further clarifies the causes of high water cut in fractured-vuggy carbonate reservoirs and explores rational and feasible management strategies to improve the current water flooding situation and reduce the comprehensive water cut in oil wells. In this paper, numerical simulation technology is used to establish a mechanism model based on the actual reservoir conditions. By comparing the development effects of four bottom water suppression measures, including the adjustment of flow channel, artificial barriers, adjustment of flow potential and gas injection, the optimal measure is selected and the relevant parameters are optimized. Building upon this, further optimization of water injection methods is conducted to explore comprehensive management strategies for enhancing the water flooding effect during high water cut periods. The research demonstrates that bottom water can be effectively inhibited by artificial barriers, leading to an expansion of the swept volume of water injection and achieving the goal of improving the high water cut condition in carbonate reservoirs. Optimal implementation of artificial barriers occurs when the water cut reaches around 80%. Specifically, positioning barriers at the bottom of perforations and setting the barrier radius at 0.15–0.2 times the well spacing obtain the most favorable results. Additionally, short-term injection with long-term shut-in, identified through cyclic water injection simulations, exhibits superior oil recovery enhancement. Validation conducted in a practical field of a fractured carbonate reservoir over a five-year period has led to a substantial increase in oil production by 5.6 × 104 t and a 12% reduction in water cut. The research approach and methodology presented in this paper can provide valuable insights and serve as a reference for the development of high water cut periods in fractured-vuggy carbonate reservoirs.