The invention discloses an isolation disc design method and system based on Allegro software. The isolation disc design method based on the Allegro software is characterized by comprising steps of: S11, capturing the coordinates of a high-speed differential signal through hole through the Allegro software, S12, detecting different wiring leading-out layers of the high-speed differential signal, and S13, automatically drawing corresponding isolation disc patterns according to the captured coordinates of the high-speed differential signal through hole and the detected reference layers where thedifferent wiring leading-out layers are located. A through hole for impedance control is realized in the design of a high-speed and high-density backboard or plug-in board, automatic coordinate capturing is carried out, the corresponding shared isolation disc is drawn according to requirements, the adjacent reference planes of the signal lines are automatically judged, the isolation disc with thesignal line protection structure meeting the design requirements is drawn, and the problems that according to a traditional design scheme, the manual drawing efficiency is low, and errors are prone tooccurring are solved.