This paper is the result of oil and gas exploration engineering. Objective The research of deep–water debris flow deposition of the Mid–Late Jurassic Lagongtang Formation on the northern margin of the Lhasa Block is important for the reconstruction on the Mesozoic tectonics–palaeogeography in the southern Qinghai–Tibetan Plateau. Methods This study conducted field investigations and microstructural analyses on the debris flow deposition of the Lagongtang Formation in the Nagqu area, and discussed its controlling factors and transport processes with previous regional geological data, and further established its depositional model. Results The lower part of the debris flow deposition consists mainly of gravelly debris flow deposits, while its upper part is characterized by sandy debris flow deposits alternating with muddy debris flow deposits, containing abundant slip collapse and sliding bodies and have a typical double structure of soft deposition. The soft depositional deformation folds and pudding structure indicate the southward flow of the debris flow. Conclusions This study indicates that the formation of the Lagongtang Formation is controlled by the Bangonghu–Nujiang suture zone, and the "source–drain–sink" of different kinds of debris flow deposition shows coupling relationships to a certain extent. The study also provides new information on the reconstruction on the structure–paleogeography of the southern Qinghai–Tibetan Plateau in Mesozoic.