The present disclosure provides a method for manufacturing a board-to-board connection structure. The method includes defining a first through hole in a first circuit board, disposing a first connector within the first through hole by a first conductive paste, and connecting the first connector to a second circuit board on which a second connector is installed, thereby realizing a connection of the two circuit boards, and reducing a height of the two circuit boards after the connection. That is, the height of the board-to-board connection structure is reduced. Additionally, since the first connector is received within the first through hole, the first connector is not easy to be damaged and oxidized. The present disclosure further provides a board-to-board connection structure manufactured by the above method.