The theoretical researches on fabrication, measurement and identification of laser marking system of 3D(three-dimension) anti-counterfeiting identifiers have been done in this paper. 3D identifiers were fabricated and 3D identifiers’ modelings were reconstructed, and binary coding of gray images were encoded by programmable control of liquid crystal mask, spatial modulating of laser beam and photolithography fabrication technics. We regarded the depth of 3D identifiers as anti-counterfeiting information, and the original marking data and anti-counterfeiting information are saved in remote database server by database technology and computer network technology，so true produces can be distinguished from fake through network. The basic theory of 3D nondestructive anti-counterfeiting identifiers based on liquid crystal mask was built, and a new technology of creating 3D anti-counterfeiting identifiers by laser shock wave was set up, which differs entirely from marking by laser ablation (or laser thermal effect). A new high-efficiency theory of detecting and identifying on 3D anti-counterfeiting identifiers by 3D identifiers’ reconstruction and binary coding was set up. The study enriches dynamic plastic deformation theory of partial high-strain-rate and anti-counterfeiting design & manufacturing theory which is also a highlight based on advanced manufacturing theory of mechanical effect on laser shock wave.