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During the burial of mudstones, the associated organic matter undergoes gradual thermal maturation, a key process that can influence the reactivity of organic matter during catagenesis, the formation of hydrocarbon deposits and the chemical weathering of mudstones. Conventional methods for assessing the thermal maturity of organic matter often fail to reflect the geochemical heterogeneity between individual organic phases in mudstone samples. Here, we report an alternative, non‐destructive, surficial and micro‐scale (analytical spot size of ~ 300 nm with about 4 μm diffusion depth for micrometre‐size organic grains) method to evaluate the thermal maturity of organic matter in mudstones using the carbonKα X‐ray spectrum measured by field emission‐electron probe microanalyser (FE‐EPMA). Using this method, we observed correlations between parameter values derived from FE‐EPMA spectra, including the peak position, the peak area and the intra‐sample heterogeneity of these measurements, and independently measured vitrinite/solid bitumen reflectance for a suite of mudstones, representing different age, geological context and burial depth. With the increased values in peak area and position, we identified an increase in the carbon mass fraction of organic matter and the mean nominal oxidation state of carbon approaching zero. These trends, which are consistent with aromatisation and graphitisation, provide the rationale for using FE‐EPMA to estimate the thermal maturity of organic matter. To explore some of these trends in more detail, we employed time‐of‐flight secondary ionisation mass spectrometry, X‐ray photoelectron spectroscopy and optical reflectance measurements on a subset of samples.