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Purpose: Wafer bonding is a key process for 3 D advanced packaging of integrated circuits. It requires very high accuracy for the wafer alignment. To solve the problems of large movement stroke, position calibration error and low production efficiency in optical alignment, this paper aims to propose a new wafer magnetic alignment technology (MAT) which is based on tunnel magneto resistance effect. MAT can realize micro distance alignment and reduces the design and manufacturing difficulty of wafer bonding equipment. Design/methodology/approach: The current methods and existing problems of wafer optical alignment are introduced, and the mechanism and realization process of wafer magnetic alignment are proposed. Micro magnetic column (MMC) marks are designed on the wafer by the semiconductor manufacturing process. The mathematical model of the space magnetic field of the MMC is established, and the magnetic field distribution of the MMC alignment is numerically simulated and visualized. The relationship between the alignment accuracy and the MMC diameter, MMC remanence, MMC thickness and sensor measurement height was studied. Findings: The simulation analysis shows that the overlapping double MMCs can align the wafer with accuracy within 1 µm and can control the bonding distance within the micrometer range to improve the alignment efficiency. Originality/value: Magnetic alignment technology provides a new idea for wafer bonding alignment, which is expected to improve the accuracy and efficiency of wafer bonding. [ABSTRACT FROM AUTHOR]