The invention discloses a self-conveying water-stone separation type flood drainage aqueduct and a construction method, and belongs to the technical field of disaster prevention and control for geotechnical engineering. The self-conveying water-stone separation type flood drainage aqueduct comprises an aqueduct inlet, an aqueduct outlet, a self-conveying aqueduct body, foundations, supporting columns and a water outlet pipe. The self-conveying aqueduct body is composed of a double-layer U-shaped channel, water turbines, driving wheels, driven wheels, belts and a conveyer belt, wherein the middle of the bottom of the upper layer of the double-layer U-shaped channel is provided with rollers, the two ends are provided with carrier rolls, the carrier rolls are provided with the driven wheels in a nesting manner, the water turbines are installed on the lower layer of the double-layer U-shaped channel and provided with the driving wheels in an embedding manner, the belts connect the drivingwheels with the driven wheels, and the rollers and the carrier rolls are sleeved with the conveyor belt. The foundations are built at the intersection of a gully and a highway, the supporting columnsare built on the foundations, the self-conveying aqueduct body is erected on the supporting columns and connected with the aqueduct inlet and the aqueduct outlet, and the water outlet pipe guides water into a gutterway. According to the self-conveying water-stone separation type flood drainage aqueduct, water and stones in a debris flow are largely separated, the kinetic energy of the water is utilized to drive the conveyor belt to convey the stones, the situation that stones settle in the aqueduct and block the aqueduct, the debris flow spills over, and the normal use of a line is affected isavoided, and the safety of pedestrians and vehicles is protected.