An aircraft center wing box digital assembly positioning system and positioning method are provided. A digital flexible positioning tool is divided into a bed body unit, a front spar positioning unit,a rear spar positioning unit, a left wing rib conformal unit, a right wing rib conformal unit, an upper tooling positioning pressing unit and a lower tooling positioning pressing unit according to functional modules. At first, an automatic positioning method is performed with the skeleton as the reference; skeleton parts such as the front spar, the rear spar and the wing rib of the large-scale central wing box are accurately positioned, and then the upper panel, the low panel and the longitudinal spar are positioned with the skeleton as a reference until the whole positioning process of the central wing box is completed. The digital assembly positioning system and positioning method are capable of accurate positioning, automatic control, multi-functional integration, and flexible design of large-scale center wing boxes.