In order to reveal variation of mechanical properties of hepatoma cells with nanometer resolution, atomic force microscopy (AFM)-based nanoindentation experiments are performed on hepatoma cell to derive Young’s modulus employing a corrected Hertz model. Under load conditions of nanoindentation force as 0.43809-0.73015nN and penetration rate as 0.4 Hz, the calculated value of Young’s modulus of hepatoma cells is 34.137±0.67kPa with a 95% confidence interval. The results demonstrate the Young’s modulus varies with the measurement position, and the center of cell possesses lower value than peripheral region. Variation of Young’s modulus is resulted from external reaction, which supports well the theory of cytoskeleton structure. Furthermore, the difference of Young’s modulus between normal cells and cancerous ones are also discussed, and it will provide possibility of a new route for early diagnosis of hepatoma.