The invention discloses a formwork fixing system of a building waterproof structure and a construction method of the waterproof structure. The formwork fixing system comprises a first formwork fixing device, the first formwork fixing device comprises a first formwork fixing clamp, a second formwork fixing clamp, distance adjusting plates and adjusting bolts; the first formwork fixing device and a second formwork fixing device both comprise first fixing device bodies; the distance adjusting plates comprise adjusting plate bodies, and strip-shaped adjusting holes are formed in the adjusting plate bodies; one ends of the distance adjusting plates are fixedly connected with one of the first formwork fixing clamp and the second formwork fixing clamp; and one ends of the adjusting bolts are fixedly connected with the formwork fixing clamp which is not connected with the distance adjusting plates and used for adjusting the distance between the first formwork fixing clamp and the second formwork fixing clamp. The formwork fixing system of the building waterproof structure and the construction method of the waterproof structure have the beneficial effects that mounting is convenient, the turnover rate and the universal rate are high; and for different projects, erecting construction of formworks can be achieved only by choosing suited formwork fixing device combinations according to needs, and then concrete is poured.