The invention discloses a PCB interlayer deviation alignment datamation analysis method and management and control system. The method includes steps of alignment capability data of adjacent layer deviation and integral layer deviation of a PCB semi-finished product after layer lamination through datamation detection by utilizing an X-ray transillumination method; detecting alignment capability data of the PCB semi-finished product after outer layer etching by utilizing an electrical property open and short circuit method; based on the alignment capability data of adjacent layer deviation and integral layer deviation of the PCB semi-finished product and alignment capability data of a finished product, analyzing the alignment capability level of different products in different technical routes systematically according to design structures, production equipment and technical processes of different PCB products. According to the invention, accurate adjacent layer deviation and integral layer deviation data can be provided for the PCB semi-finished product; accurate integral alignment data can be provided for the PCB finished product; alignment capability level of different products in different technical routes can be analyzed and provided systematically for a PCB enterprise and guidance is provided for novel product manufacture and a direction for improving alignment capability is pointed out.