The invention relates to a cloud system structure pre-warning system and method for riverway type reservoir tributary bay water bloom. The cloud system structure pre-warning system comprises a monitoring cloud module, an information cloud module, an application supporting module, a water bloom pre-warning module and a discussion decision-making module. The monitoring cloud module is composed of a field information collecting unit and an operation communication unit, storage media of the information cloud module are composed of movable distributed storage station nets combined fixedly, the application supporting module is composed of a basic supporting unit, an application customization unit, a data cooperation unit and an emergency response module, the water bloom pre-warning module is composed of a risk analysis unit and a pre-warning and forecasting unit, and the discussion decision-making module is used for achieving decision-making discussion and information sharing communication in a cloud environment. The cloud system structure pre-warning system and method for riverway type reservoir tributary bay water bloom achieve seamless linkage and operation control over the modules based on a cloud system structure, carry out all-weather monitoring, cloud storage and water bloom risk pre-warning on the inducing factors of the riverway type reservoir tributary bay water bloom and water bloom biochemical properties, and provide a new measure based on the cloud system structure for preventing and reducing water bloom events.