In order to study the mechanical properties of shale samples from Bakken Formation, nanoindentation method, an imaging technique borrowed from other engineering disciplines, was used. Different types of nanoindentation curves were analyzed and the applicability of the nanoindentation theories to study mechanical properties of shale samples at nanoscale was demonstrated. Elastic modulus and Hardness of different samples were calculated, compared and related to their mineral compositions and microstructures which are detected by 2D XRD and FESEM methods, respectively. Results showed that samples with more clay minerals (mainly composed of illite) and larger pore structures have less Young's modulus. In addition, based on the energy analysis method, the fracture toughness at nanoscale was estimated and its relationships with Young's modulus was quantified. It was observed that fracture toughness increases linearly with Young's modulus. This paper presents the results and main findings of this study.