Mudstones and shales serve as natural barrier rocks in various geoenergy applications. Although many studies have investigated their mechanical properties, characterizing these parameters at the microscale remains challenging due to their fine-grained nature and susceptibility to microstructural damage introduced during sample preparation. This study aims to investigate the micromechanical properties of clay matrix composite in mudstones by combining high-speed nanoindentation mapping and machine learning data analysis. The nanoindentation approach effectively captured the heterogeneity in high-resolution mechanical property maps. Utilizing machine learning-based k-means clustering, the mechanical characteristics of matrix clay, brittle minerals, as well as measurements on grain boundaries and structural discontinuities (e.g., cracks) were successfully distinguished. The classification results were validated through correlation with broad ion beam-scanning electron microscopy images. The resulting average reduced elastic modulus (Er) and hardness (H) values for the clay matrix were determined to be 16.2 ± 6.2 and 0.5 ± 0.5 GPa, respectively, showing consistency across different test settings and indenter tips. Furthermore, the sensitivity of indentation measurements to various factors was investigated, revealing limited sensitivity to indentation depth and tip geometry (when comparing Cube corner and Berkovich tip in a small range of indentation depth variations), but decreased stability at lower loading rates. Box counting and bootstrapping methods were applied to assess the representativeness of parameters determined for the clay matrix. A relatively small dataset (indentation number = 60) is needed to achieve representativeness, while the main challenges is to cover a representative mapping area for clay matrix characterization. Overall, this study demonstrates the feasibility of high-speed nanoindentation mapping combined with data analysis for micromechanical characterization of the clay matrix in mudstones, paving the way for efficient analysis of similar fine-grained sedimentary rocks.