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Magnetic nanoparticles (MNPs) are often used as drug-carrying particles for targeted therapy of tumors. Studying their effects on cell activity and mechanical properties is of great significance for the targeted treatment of tumors. In this paper, we used a combination of atomic force microscopy (AFM) and fluorescent labeling to study the mechanical properties of cells after the endocytosis of MNPs. Colon cancer cells SW480 were selected to co-culture with MNPs with a particle size of 50 nm, and the cell viability was measured and systematically analyzed under different conditions. The results showed that the safe dose of MNPs to colon cancer cells SW480 was 50 µg/mL, and when the amount exceeded 50 µg/mL, the cell viability decreased significantly. Increase the concentration of MNPs step by step within the safe dose of 0-50 µg/mL. Through the analysis of a large number of data measured by AFM, the results show that the mechanical properties of cells change significantly with the increase of MNPs concentration. In this paper, the experimental results are analyzed by comparing concentration gradients. The concentrations are set to 0, 30, and 50 µg/mL , respectively, to verify the influence of MNPs on the mechanical properties of cells.