The invention discloses a treatment method of a water body in a coal mine underground reservoir. The method comprises the following steps: 1 dividing a water body into a suspended solid over-standard water body, a heavy metal over-standard water body and an organic matter over-standard water body according to the water conditions of water bodies entering the underground reservoir from different underground mine water sources; 2 correspondingly dividing the underground reservoir into a suspended solid pollution treatment reservoir for removing suspended solids, a heavy metal pollution treatment reservoir for removing heavy metals and a reagent treatment reservoir for removing organic matters and inorganic matters through reagents; and 3 introducing the suspended solid over-standard water body into the suspended solid pollution treatment reservoir, processing the suspended solid over-standard water body into a qualified water body through direct filtration, introducing the heavy metal over-standard water body into the heavy metal pollution treatment reservoir, processing the heavy metal over-standard water body into a qualified water body through a modular water treatment method, introducing the organic matter over-standard water body into the reagent treatment reservoir, and processing the organic matter over-standard water body into the qualified water by adding a reagent.