In the present study, the indentation testing with a flat cylindrical indenter on typical multi-layer material systems was simulated successfully by finite element method. The emphasis was put on the methods of extracting the yield stresses and strain-hardening modulus of upper and middle-layers of three-layer material systems from the indentation testing. The slope of the indentation depth to the applied indentation stress curve was found to have a turning point, which can be used to determine the yield stress of the upper-layer. Then, a different method was also presented to determine the yield stress of the middle-layer. This method was based on a set of assumed applied indentation stresses which were to be intersected by the experimental results in order to meet the requirement of having the experimental indentation depth. At last, a reverse numerical algorithm was explored to determine the yield stresses of upper and middle-layers simultaneously by using the indentation testing with two different size indenters. This method assumed two ranges of yield stresses to simulate the indentation behavior. The experimental depth behavior was used to intersect the simulated indentation behavior. And the intersection corresponded to the values of yield stresses of upper and middle-layers. This method was also used further to determine the strain-hardening modulus of upper and middle-layers simultaneously.