The invention relates to an in-situ biological-ecological recovery integrated system for an urban river water body. The in-situ biological-ecological recovery integrated system is capable of effectively preventing the problems of unqualified fluvial cross section water body and aquatic ecosystem damage and further improving the landscape effect. According to the technical scheme adopted by the invention, the method is as follows: close-to-nature riverside buffer zones are constructed on side banks of a river reach from upstream to downstream; the river reach, at which the close-to-nature riverside buffer zones are positioned, is internally and sequentially provided with a pretreatment unit, a first ecological floating bed unit, a first ecological filtration dam unit, an aquatic plant unit, a second ecological floating bed unit, a second ecological filtration dam unit, a biomembrane-enhanced purification unit including a plug-flow aeration unit, a habitat improvement unit and an aquatic organism functional group construction zone from upstream to downstream. The in-situ biological-ecological recovery integrated system does not need to occupy land area except for a riverway, is stable in treatment effect, does not influence drawing off of floodwater in the riverway, can be used for solving the problems of unqualified fluvial cross section water body and aquatic ecosystem damage and improving the landscape effect, and has great economical and social benefits.