Palustrine‐lacustrine carbonates of the well‐dated Xichagou section (ca. 43 to ca. 13 Ma) next to the active Altyn Tagh Fault (ATF) are investigated in terms of abundance, lithofacies, strontium, carbon and oxygen isotopes, to differentiate tectonic and climatic controls on the evolution of intermontane lakes in the Tibetan Plateau. Volumetrically dominant siliciclastic strata document five depositional stages: mid‐Eocene alluvial fan (onshore), late Eocene fan delta (nearshore), Oligocene semi‐deep lake (offshore), early Miocene braided fluvial delta (nearshore) and mid‐Miocene fluvial plain (onshore). Carbonates are most abundant in the middle three lacustrine stages and contain various lithofacies, including calcretes, microbialites, grainstones and marlstones. Oxygen isotopes show two positive excursions (−1.17‰ and −2.59‰) at the first nearshore and late offshore stages, indicating two relatively saline stages linked to the Eocene and late Oligocene global warming climates. Carbon isotopes show a positive excursion (from −4.0‰ to +2.9‰) at the middle semi‐deep lake stage and meanwhile strontium isotopes of carbonates show a large negative excursion (from 0.7120‰ to 0.7113‰), both in response to the early Oligocene global humid and cooling climate and resultant lake expansion at the Qaidam Basin. Except for this lake expansion event, the first‐order lake transgressing, shallowing and regressing evolution at the Xichagou section were not consistent with Cenozoic global climatic change trends. Instead, the two‐stage strike‐slip faulting of the ATF probably induced the northeastward and eastward migration of basin depocenter and resulted in the lake transgression‐regression at the Xichagou section. The widespread presence and relatively minor variation in oxygen isotopes (from −7.5‰ to −7.0‰) of early Miocene microbialites in the northern Tibetan Plateau suggest a warm climate and a low relief before ca. 15 Ma.