The invention relates to an alignment system and alignment method having a focusing function. The system comprises an alignment imaging unit, a signal processing and control unit and a workpiece table, wherein the workpiece table is used for bearing a silicon wafer, alignment marks are arranged on the silicon wafer, the alignment imaging unit comprises a lighting unit, a phase shift mark and a detection unit, the phase shift mark has phase difference, the detection unit is used for detecting imaging information of the alignment marks on the silicon wafer and detecting imaging information of the phase shift mark, the phase shift mark and a silicon wafer surface of an optimal focus surface are in an imaging conjugation relation, and the signal processing and control unit is used for processing the imaging information of the phase shift mark to obtain defocusing information of the alignment imaging unit, controlling the workpiece table to perpendicularly move according to the defocusing information and the imaging information of the alignment mark and moving the alignment mark on the workpiece table to an optimal focus surface position. The phase shift mark with certain phase difference is used for automatically focusing in an imaging mode, the defocusing quantity is converted to horizontal movement of an image of the phase shift mark, and the adaptability of the alignment system is improved.