The Lower Cretaceous sedimentary strata in the Lhasa Terrane record the palaeogeographic and tectonic history of the Tibetan Plateau prior to the India-Asia collision. The Lower Cretaceous strata in the Coqen Basin of the northern Lhasa subterrane include the Duoni and Langshan Formations. The Duoni Formation is composed of conglomerates, sandstones, siltstones and mudstones in the south deposited in a fluvial environment and quartzose-lithic sandstones, siltstones and mudstones in the north deposited in a shelf-coastal environment. The overlying Langshan Formation is characterized by abundant Orbitolina- and rudist-bearing wackestones and packstones, which were deposited on a low-energy carbonate ramp. The Langshan Formation in the Coqen Basin was deposited between ~ 119–115 Ma and ~ 98 Ma based on its large benthic foraminiferal assemblages. Age constraints based on the interbedded tuff and conformably overlying Langshan Formation indicate that the Duoni Formation was deposited between ~ 123 and 115 Ma. Sandstone detrital modal compositions further indicate that the Duoni Formation was primarily derived from magmatic arc and recycled orogen sources. Detrital zircons from the Duoni Formation yield a primary age population of 160–110 Ma (peaking at ~ 130 Ma), with negative εHf(t) values (− 18.7 to − 2.7), and additional age ranges of 550–500, 1200–900, and 1600–1500 Ma, thereby indicating that the Zenong volcanic rocks and Palaeozoic sedimentary bedrocks in the northern Lhasa subterrane are the most likely sources. The palaeogeography of the northern Lhasa subterrane can be approximately described in two stages. During the Aptian (~ 123–115 Ma), with the eruption of the Zenong volcanic rocks, the Duoni Formation accumulated in fluvial and shelf-coastal environments and was sourced from the Zenong volcanic rocks and basement rocks from the southern region of the northern Lhasa subterrane. The enhanced magmatic activities in the northern Lhasa subterrane may have influenced the Duoni Formation deposition. During the Late Aptian-Early Cenomanian (~ 115–98 Ma), a north-south transgression occurred, causing the majority of the northern Lhasa region to be dominated by shallow-marine limestones of the Langshan Formation.