Warship damage flooding is the interactive process between progressive flooding and counter-flooding on the battle damage condition. However, traditional damage stability theory couldn’t simulate the influence of counter-flooding on damaged warship flooding process. There isn’t the method to predict damaged warship flooding process in the full-time. By proposing the coupling relationship between damage flooding process and counter flooding activities, the damage stability full-time domain model taking counter-flooding into account is established, and the numerical solving algorithm is given. Case study is analyzed based on the model and algorithm. Visual and interactive simulation system is developed. The research achievement is capable of assessing the flooding process and various counter-flooding comprehensively, and is an important supplement for warship damage stability theory. The achievement can help designer understand the effectiveness of counter-flooding design scheme on flooding process, and guide the design of counter-flooding system. In addition, the achievement can be used for shipboard flooding decision-making, and has high military application value.