Tracing interactions during burial-induced organic maturation and associated clay-material alteration is of prime importance for understanding both the individual and combined mineral and organic processes. In the present study the light elements B, Li, O, and H of a sample from oil-prone Eocene Kreyenhagen Shale from San Joaquin Basin (California) were examined. The natural burial-induced temperature increase was simulated by pyrolysis experiments at progressively increasing temperatures (270–365°C) and for varied durations (72–216 h) applied to the whole rock and its <2 μm fraction. The illite structure as well as the K-rich interlayers of the illite-smectite mixed layers were not affected by the pyrolysis experiments and the smectite-rich interlayers did not collapse, while the soluble minerals and the organic matter were altered. The distribution pattern of the rare-earth elements (REEs) from untreated whole rock and of its pyrolyzed equivalents are within analytical uncertainty, which confirms that the changes induced by pyrolysis experiments were minimal in the bulk sample. Conversely, the REEs from the <2 μm fractions were modified significantly, suggesting that the whole rocks and the <2 μm fractions may contain different types of organic materials. Also, only the carbonates, oxides, chlorides, and organic matter were affected together with the smectite-rich interlayers of the illite-smectite structure. Bitumen coating of the smectite interlayers probably increased the amount of B of organic origin in their sites. The δ11B and δ7Li of the successively expelled hydrocarbon phases changed with increasing pyrolysis temperatures, together with the B and Li contents of the hydrocarbon-related fluids. On the basis of the δ11B and δ7Li from pyrolyzed clay fractions, the B released successively was not isotopically homogeneous, probably depending on how the type of organic matter decomposed during the successive pyrolysis steps, and on which components were released. The δ11B of organic-B increased progressively from –2‰ at low experimental temperature up to +9‰ at the highest temperature. The calculated δ7Li that was released also increased relative to the value of the outcropping sample used as a reference, but it remained almost constant from –7‰ at 310°C for 72 h to –8‰ at 365°C for 216 h. The δ18O values of the <2 μm size fractions decreased significantly during pyrolysis above 300°C, but the δD changes were rather modest. The total organic carbon (TOC) remained statistically constant after pyrolysis to 300°C, as did the δ7Li values. The pyrolysis experiments in the present study suggest the presence of bitumen-coated smectite interlayers that could have been misidentified as dehydrated smectite in the literature. Together with abnormal illite K-Ar ages, the occurrence of such bitumen-coated illite-smectite interlayers occurring in source and reservoir rocks could indicate the timing of hydrocarbon maturation relative to illitization.