The invention relates to a precast concrete box type structure and cast-in-place concrete combined type water gate pier structure and a construction process thereof, and belongs to the technical field of construction of water gates. Firstly, reinforced concrete members are prefabricated in a partitioning mode on a prefabrication site according to the outer size of a water gate pier; after the prefabricated members are transferred nearby a gate pier foundation on site, the prefabricated members are hoisted in place and connected layer by layer through hoisting equipment, and the box type gate pier structure is formed through installation layer by layer; and rebar binding and concrete pouring are carried out in the box type structure layer by layer. Through layer-by-layer installation of the gate pier prefabricated members, and layer-by-layer rebar binding and concrete pouring, the water gate pier is built finally. By adopting the construction method, the time of on-site construction of a water gate is shortened, the total construction progress of the water gate project is accelerated, and the water gate project which needs to be completed in two dry seasons in the past can be completed in one dry season. Thus, the design functions of flood control, power generation, navigation and the like can be completed in advance, and the project can achieve the functions and the benefits soon.