The invention discloses a multi-center watershed water environment distributed cluster management system and method. The system creates a system operation management center, a numerical simulation center, a data center, a decision command center and a client-side service center, all of which are of different management levels and function levels. By means of division and cooperation of the different centers, computer resources of centers of units of the watershed water environment can be integrated, a resource pool is formed, services are provided according to demands of functions of the centers of the units of the watershed, the problems, such as waiting time losses, the low watershed scale simulation computing speed, low efficiency and resource waste for repeated construction, of a traditional watershed model system due to serial computation can be solved, the watershed water environment simulation efficiency is greatly improved, hardware resources and data resources of the whole watershed are integrated, water environment management, current situation evaluation, future trend prediction and sudden event emergence simulation and decision support of the whole watershed are achieved, and safety of the watershed water environment is guaranteed.