The invention discloses an engineering surface layer watertight template structure and a construction method thereof. The watertight template structure comprises an expansion joint and building bodieslocated on the two sides of the expansion joint. Concave portions are arranged at the positions, close to the expansion joint, of the building bodies, so that the joint of the building bodies and theexpansion joint is in a step shape; each concave portion is sequentially provided with a first plane, a second plant and a third plane from interior to exterior, wherein the first plane and the thirdplane are parallel; a watertight template is arranged between the two concave portion, the watertight template comprises a groove plate with the U-shaped section, the groove plate is located at the expansion joint, and an opening of the groove plate faces the expansion joint; the two ends of the groove plate are each sequentially connected with a first board, a second board and a third board, wherein the inner end face of the first board is flushed with the first plane, the inner end face of the second board is flushed with the second plane, and the inner end face of the third board is flushed with the third plane. The surface grooving quality of the expansion joint is convenient to control, the surface layer grooving technology of the expansion groove is improved, and the final watertight effect for hydraulic structure expansion joint surface layer watertight is improved.