The invention provides a hollow pier prefabricated inter-segment connecting device and a construction method thereof.The connecting device comprises embedded steel plates, U-shaped steel bars, rubberplates, upper/lower connecting steel plates, upper/lower shear-resistant steel plates and filling plates, the embedded steel plates are embedded in the inner surfaces of prefabricated segments, the U-shaped steel bars are welded to the embedded steel plates, parts of the U-shaped steel bars extend into the prefabricated segments, and parts extend out of the embedded steel plates; threads are arranged on the extending portions, and the rubber plate, the upper connecting steel plate and the lower connecting steel plate are connected with the embedded steel plate through connecting bolts. And after the upper prefabricated segment and the lower prefabricated segment are assembled, the upper shear-resistant steel plate is connected with the upper connecting steel plate through high-strength bolts, the lower shear-resistant steel plate is connected with the lower connecting steel plate through high-strength bolts, filling plates are plugged between the upper shear-resistant steel plate and the lower shear-resistant steel plate, and the upper shear-resistant steel plate is connected with the lower shear-resistant steel plate through high-strength bolts. The connecting device disclosed bythe invention meets the requirements of different procedures in the assembling process of the prefabricated sections, and realizes the functions of hoisting, section position positioning, section linear adjustment, section glue joint prepressing, temporary locking and the like.