The invention relates to the field of water conservancy project buildings in civil engineering, in particular to an embedded groove type aqueduct water-stop structure. The embedded groove type aqueduct water-stop structure comprises a rubber water-stop belt 1. A U-shaped structure 11 is arranged on the rubber water-stop belt 1. An acrylic emulsion mortar block 7 is used on an upstream face 12 of the rubber water-stop belt 1 for sealing. Protrusions 8 are arranged on the two sides of the U-shaped structure 11 on a downstream face 10 of the rubber water-stop belt 1. Embedded grooves 2 are formed in the lower faces of the protrusions 8. The high requirements of a traditional binding mode or pressing plate type water-stop structure on a concrete base face are weakened, the problem that traditional water-stop structure bolt embedment accuracy is not easy to control is solved, fastening force is guaranteed, and later-period maintaining and replacing are convenient. The invention further discloses a construction method of the embedded groove type aqueduct water-stop structure.