The Donglin Coal Mine, an important mine in the Nantong coalfield in southwestern Chongqing, is immediately adjacent to the Songzao coalfield. To investigate the mineralogy and geochemistry of Donglin coals, profile channel samples from the mineable Nos. 4 and 6 coals were collected. The minerals, major element oxides, and trace elements were analyzed by LTA-XRD in combination with Siroquant software, XRF, ICP-MS, ICP-CCT-MS (As and Se), ISE (F), and DMA-80 Hg analyzer (Hg). The results indicate that the Donglin low volatile bituminous coals were characterized by low ash yields and high total sulfur contents. The minerals varied between the Nos. 4 and 6 coals, differentiated by montmorillonite, calcite, ankerite, and pyrite. Despite the low boron concentration, Donglin coals were influenced by brackish water during coal accumulation. Selenium (10.9 mg/kg), F (431 mg/kg), Hg (0.350 mg/kg), Nb (20.7 mg/kg), and Ta (3.68 mg/kg) in the No. 4 coals, and F (425 mg/kg), Be (7.11 mg/kg), Ga (14.5 mg/kg), Ge (22.5 mg/kg), Zr (218 mg/kg), Nb (35.5 mg/kg), and Ta (4.42 mg/kg) in the No. 6 coals are slightly enriched. Four vertical distributions of elements were demonstrated, i.e., roof, floor, roof and floor, and middle enrichments. The slightly enriched trace elements and UCC-normalized REY distribution patterns of the Donglin coals jointly eliminated the impact of various volcanic ashes and terrigenous input from the Kangdian Oldland during the Late Permian. However, the roof rock samples shared the geochemical feature of mafic tonstein (enriched Sc, V, Cr, Co, and Ni), while the floor rock of the No. 6 coals resembles alkali tonsteins (enriched Ga, Zr, Nb, Ta, Hf, and REY). Lithium, Ga, Zr, Ag, Cd, In, Sn, Cs, Hf, Bi, Th, and U occurred in kaolinite and/or montmorillonite in the No. 4 coals, while Li, Nb, Ag, Cd, In, Cs, Ba, and Th occurred in kaolinite in the No. 6 coals. Vanadium, Sr, and Mo in the No. 4 coals, and Sr and Sc in the No. 6 coals were associated with calcite and/or ankerite. Arsenic, Se, Hg, Sb and Tl, and Hg and Mo were associated with pyrite in the Nos. 4 and 6 coals, respectively. Lithium, Be, Ge, and Sb in the No. 4 coals and Be and Ge in the No. 6 coals might be of organic affinity.