The invention relates to the field of urban rainwater treatment systems, in particular to a separate system pipe network based area fragmented rainwater abandoned flow treatment system. An area internally comprises a sewage header pipe, rainwater branch pipes and sewage branch pipes; the discharging ends of the sewage branch pipes are communicated with the sewage header pipe, the area is divided into a plurality of segments in a grid shape, and the area of each fragment is 0.2-4 square kilometers; each fragment is internally provided with a sewage branch pipe, a rainwater branch pipe and one or more abandoned flow wells; each abandoned flow well comprises a well body, each well body is provided with a water inlet pipe communicated with the discharging end of the corresponding rainwater branch pipe, a water outlet pipe communicated with natural water and an abandoned flow pipe communicated with the sewage header pipe. The separate system pipe network based area fragmented rainwater abandoned flow treatment system is simple in structure, the problem of delay in the long-distance conveying process of initial rainwater in the prior art is solved through the independent abandoned flow wells in the fragments, the treatment pressure of a sewage treatment plant is relieved, the situation that initial rainwater pollutes natural water is further avoided, and discharging treatment of rainwater is more reasonable and effective.