The invention discloses a construction method of an in-water pier and a pier top beam section of a bare rock riverbed. The construction method comprises the steps that first, a trestle is erected; second, a cofferdam is constructed; third, steel protective cylinders are mounted; fourth, cofferdam bottom-sealing construction is conducted; fifth, the cofferdam is anchored, specifically, the steel cofferdam is anchored through a prestressed anchoring device; sixth, bored piles are constructed; seventh, water in the cofferdam is pumped, and the steel protective cylinders are cut off; eighth, an in-water bearing platform is constructed; ninth, a pier body is constructed; and tenth, the pier top beam section is constructed. In the bored pile construction process in the sixth step, the in-water bearing platform construction process in the eighth step, the pier body construction process in the ninth step and the pier top beam section construction process in the tenth step, concrete pumping pipes are used for concrete conveying. The construction method is simple and convenient, the steel cofferdam and pile bodies of the bored piles are connected into a whole in a fastened mode through the prestressed anchoring device, thus the steel cofferdam is anchored on the pile bodies of the bored piles, the steel cofferdam can be effectively prevented from floating, the overturning-resistance safety factor of the steel cofferdam can be increased, and meanwhile long-distance concrete pumping can be easily and conveniently completed by using the trestle.