The quantification of mechanical properties of organic matter in shale is of significance for the fine prediction and characterization of shale reservoir's mechanical properties. Due to the micron-sized and dispersed distribution of organic matter particles in shale, the accurate evaluation of the actual mechanical response remains challenging. This work focuses on shale from Wufeng-Longmaxi Formation, which is the main shale gas exploration and development formation in China. A method based on atomic force microscopy (AFM) with an optical microscope (i.e., in-situ AFM technique) is presented to locate the organic matter in-situ and then visualize and quantify its mechanical properties using AFM Young's modulus mapping. The merits and limitations for determining the mechanical properties of organic matter in shale between the AFM and the more conventional nanoindentation technique are discussed. Results show that combining in-situ nanoindentation and in-situ AFM mapping provides more accurate description of the mechanical properties of organic matter in shale than traditional grid indentation methods with low spatial resolution. The Young's moduli of organic matter calculated from nanoindentation are around twice smaller than those obtained from AFM measurements mainly because the elasto-plastic deformation zone of organic matter in nanoindentation tests is larger and can be additionally affected by the presence of inorganic particles and/or larger micro-pores in organic matter. The Young's modulus and hardness of graptolite in the shale obtained by nanoindentation are slightly larger than those of solid bitumen at the same thermal maturity. Both in-situ AFM and in-situ nanoindentation results show that the mechanical strength of organic matter increases with increasing maturity. Overall, the presented approach shows a great potential for accurate and in-situ measurement of the mechanical properties of organic matter in shale at the nanoscale, which may be beneficial to the development of rock mechanical models for the accurate evaluation of the actual mechanical properties of shale.