Simultaneously determining the film thickness, Young’s modulus and hardness of film and substrate is a significant challenge due to the substrate effect. A method to solve the inverse problem of characterizing the mechanical properties of bilayer materials for instrumented indentation testing is proposed. This is done in combination with a weight function which could be obtained via finite element simulation. Using the proposed method, the film thickness and Young’s modulus of film-substrate materials, and the hardness values of the film and substrate could be determined. The proposed method is applicable to Vickers, Berkovich, and 70.3° conical indenters. Within the study range, numerical and theoretical results show that this method is both feasible and accurate in determining the above parameters, compared with existing experimental results. The method flow chart to determine the above parameters is also shown. This method separates the coupling effect between the film and the substrate in the bilayer material, giving it practical prospects in the field of indentation testing technology.