For multiphase advanced high strength steels (AHSS), the constituent phase properties play a crucial role in determining the overall mechanical behaviors. Therefore, it is important to accurately measure/estimate the constituent phase properties in the research of AHSS. In this study, a new nanoindentation-based inverse method that we developed was adopted in estimating the phase properties of a low alloy Quenching and Partitioning (Q&P) steel. A microstructure-based Finite Element (FE) model was also generated based on the Electron BackScatter Diffraction (EBSD) and Scanning Electron Microscopy (SEM) images of the Q&P steel. The phase properties estimated from nanoindentation were first compared with those estimated from in-situ High Energy X-Ray Diffraction (HEXRD) test and, then, employed in the generated FE model to examine whether they can be appropriately used as the input properties for the model. The results show that the estimated phase properties from the inverse method are similar to those from HEXRD, and that the Ultimate Tensile Strength (UTS) and Uniform Elongation (UE) predicted from the FE model based on the estimated phase properties are also similar to those of tensile experiment of the Q&P steel. Based on the results in this study, the nanoindentation-based inverse method appears to be a viable way in determining the phase properties of complex multiphase steels with submicrometer grain sizes.