The Hongshan and Huobuxun sags are located in the eastern segment of the northern Qaidam Basin, and the provenances of Jurassic deposits in the two sags are unclear. Based on the tectonic setting of the northern Qaidam Basin before the Jurassic, this paper discusses provenances of the two sags by field geological survey, analysis of detritus, and heavy minerals of the Jurassic strata. The Jurassic sedimentation in the Hongshan Sag mainly came from the Zongwulong Orogen and the Oulongbuluke and Kuerleike mountains, and the Xitie Mountain was the secondary provenance. The Jurassic deposits of the Houbuxun Sag mainly came from the Xitie and Aimunike and Dadakenwula mountains. Because of the barrier of the Zongwulong Orogen, the sources of Jurassic deposits from the South Qilian Caledonian Orogen were much fewer. Four Jurassic provenance systems of the Hongshan and Huobuxun sags are recognized through heavy mineral assemblages: Kuerleike–Zongwulong, Zongwulong–Oulongbuluke, Xitie, and Aimunike–Dadakenwula mountains provenance systems. Based on the provenance analysis of the two sags, the paper further discusses the basin–mountain system in the eastern segment of the northern Qaidam Basin during the Jurassic. The two sags were not an open connected basin as considered by some geologists but two isolated sags. The Kuerleike, Oulongbuluke, and Zongwulong mountains together constituted the northern sedimentary boundary of the Hongshan Sag, and the southern sedimentary boundary was the Xitie Mountain. The northern boundary of the Huobuxun Sag was the Xitie, Aimunike, and Dadakenwula mountains, which separated the Hongshan Sag from the Huobuxun Sag, resulting in the two sags to evolve independently into the faulted basins during the Jurassic.