The Wulantuga germanium deposit (WGD), with germanium(Ge) resources up to 1600 tons, is a super-large Ge deposit hosted in coal seams, which has been found in recent years. The mineralogical characteristics of Ge-bearing lignite from WGD, as well as the contemporary Ge-barren lignite from the Hongqi Coal Mine, were systematically studied by X-ray diffraction, scanning electron microscope with energy-dispersive X-ray spectrometer (SEM-EDX) and electron probe microanalyser (EPMA). The results showed that the primary minerals in the Ge-bearing lignite of WGD include quartz and montmorillonite, the secondary minerals include feldspar, kaolinite and illite, and minor gibbsite, hornblende, pyrophyllite, gypsum, chlorite, anatase, pyrite, calcite, dolomite and weddellite. SEM-EDX and EPMA analyses showed trace zircon, sphalerite, scheelite, chalcopyrite, halogenide, phosphate and Pb, Bi, Cr, As and Sb-bearing minerals exist in the Ge-bearing lignite of WGD. No Ge-bearing mineral has been detected. These results showed that Ge in Ge-bearing coal may be mainly associated with organic matter, while Ba, Zn, Ti, W, Pb, Bi, Cr, Fe, As, Zr, Sb, Cu, and REE may be mainly associated with mineral phases. Furthermore, silver-bearing particles or native Ag have been detected for the first time in Ge-bearing lignite from WGD, as well as in Ge-barren lignite from the Hongqi Coal Mine, indicating lignites from the Shengli Coalfield may contain considerable Ag mineralization.