This application provides a method for aligning single core boards of a multilayer circuit board. The method includes: first determining a precise region of a specified surface of a single core board, where the precise region of the specified surface of the single core board has a precise region target, and an auxiliary region of the single core board has an auxiliary target; mounting a single core board of a reference board to a board stacking machine; obtaining first coordinates of a precise region target and second coordinates of an auxiliary target of the single core board of the reference board; transporting an N th layer of single core board to the board stacking machine, where N ≥ 2; obtaining third coordinates of a precise region target and fourth coordinates of an auxiliary target of the N th layer of single core board; and stacking the N th layer of single core board and an (N-1) th layer of single core board, so that a deviation between the third coordinates and the first coordinates is not greater than a first specified threshold A, and a deviation between the fourth coordinates and the second coordinates is not greater than a second specified threshold B. Therefore, a layer deviation between single core boards is reduced, an overall layer deviation of a multilayer circuit board is reduced, and outgoing line density of the multilayer circuit board is increased.