The invention provides a compound type rainwater tail end treatment system and a method thereof and belongs to the technical field of sponge engineering. The system is characterized in that a four-stage rainwater filtering system is arranged at the tail end of an urban drainage end and is successively formed by an overflow well, an ecological water purification structure and a two-stage stone cagenet cofferdam structure. The compound type rainwater tail end treatment system and the method thereof have the beneficial effects that the four-stage filtering system is capable of effectively filtering and adsorbing pollutants in the tail end rainwater, rapidly absorbing the rainwater, storing the rainwater in the self structure and reducing the water loss to a maximum extent; when the externalenvironment is dry, inner gaps are used for releasing the rainwater outside through capillary action and supplying the water to the plants; the device is free of power consumption, simple in structure, reliable in effect and convenient to maintain, and is suitable for controlling the urban rainwater tail end pollution, reducing the degree of pollution of the rainwater to the urban landscape riverwater quality and restoring the river way ecological system.