The world-class coal-hosted Ge ore deposits of Wulantuga (Inner Mongolia) and Lincang (Yunnan Province) in China display unusually high concentrations of some trace elements, including Be, Ge, As, Sb, Nb, W, and U. In coal, these elements may be associated with the macerals and/or with the inorganic fraction (e.g., minerals and amorphous phases). Distinguishing among different associations is important for practical applications, but still challenging. In this study, an in situ electron probe micro-analysis (EPMA) technique was applied in order to map the distribution of both light elements (C, O, and S) and selected trace elements (Wulantuga: Ge, W, and As; Lincang: Ge, W, As, and U) in the high-Ge lignite samples and their low-temperature ashes (LTAs). The EPMA detection limit was stable for these light and trace elements commonly associated with organic matter, so that reliable point analysis data were acquired for individual macerals. Additional mineralogical and geochemical data were obtained by petrographic microscopy, XRD, EDS, and ICP-MS analyses. WDS in situ element mapping and point analysis demonstrate that the huminite in the Wulantuga coal has a lower C content and higher O and S contents relative to inertinite, and Ge, As, and W show a preferential enrichment in huminite. Among the different huminite macerals in both the Wulantuga and Lincang coals, Ge, As, W, and U tend to occur in more compact huminites (ulminite or gelinite), and their abundances show mild to considerable variations across the compact huminites. The in situ concentrations of Ge and W display a direct correlation, suggesting their co-affiliation with organic matter. Elements such as Ge, W, and U have a considerable organic affinity, with a minor fraction associated with inorganic S-rich phases, such as iron sulfide/sulfate (e.g., pyrite and copiapite). Arsenic has a mixed affinity to organic matter and iron sulfide/sulfate. No Ge minerals have been detected in the LTAs, and Ge in the LTAs is likely to exist in an inorganically amorphous state. This study could provide new perspectives on the modes of occurrence of trace elements concerned in the coal-hosted germanium ore deposits in China.