In order to reduce the influence of inaccurate area function to the measurement results of mechanical properties of thin-film and other micro-sized materials, a method to improve the accuracy of the indenter area function at small indentation depth is proposed. This method links the projected contact area between the indenter and the sample with the tip radius and angle of the indenter, which can improve the reliability of the commonly used area function determination method in the measurement of shallow indentation below 50 nm. The experimental results show that the measurement accuracy of indentation hardness and reduced modulus at a small contact depth can be improved by using this area function determination method.