Microbially mediated smectite illitization has been extensively demonstrated in laboratory experiments. Despite occasional observations in geological environments, the transformation mechanism is still poorly understood. Here we investigated a series of volcanic ash (tephra) samples from the Permo-Triassic boundary (PTB) successions of South China, using short-wavelength infrared (SWIR) spectroscopy, in combination with XRD, MIR, EPMA, SEM, TEM, and 27Al NMR analyses, in order to establish a better understanding of microbial illitization, and to test the applicability of SWIR as a monitor for this process. Mixed-layer illite-smectite (I-Sm) clays are the predominant clay minerals, with illite percentages ranging from 32 to 93%. The (060) value of I-Sm varies from 1.4956 to 1.4996Å, indicating a dioctahedral precursor smectite. The precursor smectite of I-Sm is nearly free of Fe, and is probably montmorillonite. The b-cell dimension (b0 parameter) exhibits a positive correlation with the illite percentage of I-Sm, suggesting that the illitization occurs with significant cation substitutions. The different spectroscopic results all indicate that tetrahedral Al substitutes for Si, and octahedral Al is mainly substituted by Mg and/or Fe with illitization, consistent with the findings of XRD analysis. Chemical compositions and trends in their variation show typical features of a dissolution-precipitation (DP) mechanism. The SEM images reveal abrupt changes in morphology and the TEM analyses suggest progressive changes in polytype with illitization, also supporting the DP process. The transformation mechanism of I-Sm contradicts the conventional wisdom concerning diagenetic bentonite I-Sm, similar to that of hydrothermal origin, probably as the result of to the involvement of microorganisms. The SWIR parameters, such as position, depth, area and asymmetry of the absorption bands, versus illite percentage in I-Sm, generally give good correlations. SWIR spectroscopy is demonstrated as a valuable method to identify I-Sm with different percentages of illite, and with a capability as a sensitive monitor for I-Sm structure ordering and crystal-chemistry. Thus it can be used as an alternative or complementary method in conventional I-Sm studies, as well as in epithermal and hydrocarbon-reservoir explorations and astrobiological investigations.