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Viscoelastic mechanical properties of biological cells are commonly measured using atomic force microscope (AFM) dynamic indentation with spherical tips. A semiempirical analysis based on numerical simulation is built to determine the cell mechanical properties. It is shown that the existing analysis cannot reflect the accurate values of cell elastic/dynamic modulus due to the effects of substrate, indenter tip size, and cell size. Among these factors, substrate not only increases the true contact radius but also interferes the indentation stress field, which can cause the overestimation of cell moduli. Typically, the substrate effect is much stronger than the other two influences in cell indentation; and, thus, the cell modulii are usually overestimated. It is estimated that the moduli can be overestimated by as high as over 200% using the existing analysis. In order to obtain the accurate properties of cells, correction factors that account for these effects are required in the existing analysis.