Dynamic explosion in a compartment damages the structure, resulting in flooding and even sinking of the ship. To study the flooding characteristics of damaged compartments and floating states of the hull under deformation of the bulkhead caused by explosion, the damage effects on a single compartment and multiple compartments under dynamic explosion are illustrated. Then, the flooding characteristics are analyzed for single compartment models with two types of damage modes and one multi-compartment asymmetric damage model. The results indicate that the deflection of the bulkhead increases the capacity of the compartment, resulting in variations in the flooding process of damaged compartments. Compared with the single models without deflection deformation, the final flooding quantity of the two types of models with deflection deformation increased by 62.49% and 65.48%. The difference in flooding characteristics led to deviation in the six-degree-of-freedom motion of the two types of hull models. Significantly, the amplitude of heave in the models with deflection deformation under the two types of asymmetric damage modes increased by 60% and 66% compared to that of the models without deflection deformation, and the pitch increased by 66% and 50%. Nevertheless, in the multi-compartment models, there were no distinct differences in the flooding process and six-degree-of-freedom motion. These results can support the rapid assessment of the unsinkability of ships in explosive environments.