A system for safe intelligent drainage comprises a draining main pipe, a first water falling port, a second water falling port, ..., an Nth water falling port, a first confluence point, a second confluence point, ..., and an N confluence point. The first water falling port, the second water falling port, ..., and the Nth water falling port are connected with the first confluence point, the second confluence point, ..., and the N confluence point respectively through a first drainage branch pipe, a second drainage branch pipe, ..., and an Nth drainage branch pipe, and accumulated water is sequentially drained into the draining main pipe through the water falling ports, the drainage branch pipes and the confluence points. The head end of the first drainage branch pipe is provided with a valve, head ends and tail ends of the remaining drainage branch pipes are provided with valves, the tail ends of the draining main pipe between the confluence point in the water flow direction are respectively provided with valves, and the valves are in an open state and a closed state. According to the system for safe intelligent drainage and a drainage method, water is leaked in shortest time, roofing safe drainage is not influenced, and water leakage points are selectively maintained in time.