This study summarizes the results of geological, petrographical, geochemical, and mineralogical analyses performed to determine the geological controls on coal quality of the Yili Basin in Xinjiang province, northwest China. Forty-eight coal samples were collected from boreholes Q12ZK01 and Z40ZK1, and Piliqiang and Musixiang coal mines. The difference in base subsidence rate between the coal-bearing strata Badaowan and the Xishanyao Formations determines these differences of depositional environments, swamp groundwater table, and degree of terrigenous supply. These factors may further cause the difference in coal quality. The vitrinite contents, ash yields, volatile matter yields, total mineral contents, and most element contents are higher in coals of the Badaowan Formation from the Q12ZK01 and the Musixiang mine than those of the Xishanyao Formation from the Piliqing mine and the Z40ZK1. The high volatile matter yields of the coals in the Badaowan Formation, relative to those in the Xishanyao Formation, may be due to higher content of vitrinite that contains more volatile matters. In comparison with the average concentrations for Chinese and worldwide coals, the Yili coals are enriched mainly in Ca, Na, Mg, Mn, Co, Sr, Ba, and W, but the other elements are depleted in the Yili coals. Elements including Si, Al, K, Li, Ti, Cr, Cu, Rb, Zr, Pb, and some REE (La, Ce, Pr, Nd, Sm) are predominantly associated with aluminosilicate minerals. Iron, Mg, and Mn in the coals of the Musixiang mine and Z40ZK1 are associated mainly with carbonate minerals. Sulfur, Co, and Ni in the Musixiang mine coals, and B in the coals of Q12ZK01 and the Z40ZK1 mainly show an organic affinity. Sodium in the Musixiang mine coals may occur in the brines.