β -Carotene, the precursor of β -carotane, is commonly rich in brackish sediments and would become unstable theoretically under the exposure to high temperatures, bright light conditions, and acidic or oxdizing environments. However, the specific process and mechanism of the absence of such compounds are still not clear sufficiently. To fill the knowledge gap, in this study we explore the origin of the absence of β -carotane in a 50-m-thick section of the Middle Permian Lucaogou Formation in the Jimusar Sag, Junggar Basin, northwest China, based on a combined mineralogical, petrographic, organic and inorganic geochemical study. Biomarker analyses indicate that the β -carotane-free section was deposited in a brackish, reducing, and semi-deep lacustrine environment. Hydrothermal fluid effects during sediment deposition are inferred to have caused the breakdown of β -carotene. The hydrothermal (<100 °C) effects are evidenced by mineralogy and geochemistry, e.g., the hydrothermal-indicative minerals (reedmergnerit, tuff and pyrite), high Fe/Ti and low Al/(Al + Fe) ratios, rare earth elements (REEs) distribution. Associated biomarker variations were found, e.g., low i -alkanes/ n -alkanes, high C 24 Tetracyclic/C 26 Tricyclic terpanes, high (C 19 + C 20 )/(C 21 + C 23 ) tricyclic terpanes, high C 29 /C 30 hopanes, and very low gammacerane/C 30 hopane ratios. Our data suggest that hydrothermal fluids can prevent the preservation of β -carotene, and the absence of β -carotane indicates a period of hydrothermal activity during deposition of the Lucaogou Formation in a 50-meter-thick sequence. • β -Carotanes were found to be absent in a brackish lacustrine sequence. • Hydrothermal fluids have caused the breakdown of β -carotene. • Anomalously low abundance of isomerization alkanes and high C 24 Tet/C 26 TT ratios were also found. • Hydrothermal activity was present in the Permian Lucaogou Formation, Junggar Basin. • Absence of β -carotane can be used as a proxy for hydrothermal activity.