Detailed stratigraphic and paleogeographic analyses of data from 72 boreholes for the Middle Jurassic intermontane fluvial-lacustrine coal-bearing sequences were conducted in the Yuqia coalfield of the northern Qaidam Basin, northwestern China. Three third-order sequences lasting in total ca. 10.6 m.y., and an internal lowstand systems tract (LST), transgressive systems tract (TST), highstand systems tract (HST), and falling-stage systems tract (FSST) have been identified. A series of sequence-specific paleogeographic maps have been constructed based on the contours of lithological parameters. The paleogeographic units include alluvial fan-braided (meandering) fluvial plain, upper delta plain, lower delta plain, subaqueous delta, shore-shallow lake, and deep lake. The preferred sites of coal accumulation are interdelta bays, upper delta plains, lower delta plains, and fluvial back swamps. The sequence stratigraphic and sedimentological analysis of the Middle Jurassic coal-bearing measures of the Yuqia coalfield provides a basis for a comprehensive coal accumulation model that involves a six-period evolution from the LST, early TST, late TST, early HST, late HST to FSST. The major coal seams were accumulated in the early and late TST of the sequences S1 and S2. These results are of practical significance for coal resources exploration and enhance geological effects of prospecting engineering in the northern Qaidam Basin.