The No.2-1 coal (Early Permian-Shanxi Formation) in the Lugou Mine, Xinmi coalfield, Northern China, is a characteristic tectonically deformed coal. A total of 15 coal bench samples were considered, including 13 bench samples, one roof, and one floor. In this study, the content, distribution, and occurrence of harmful trace elements and rare earth elements (REE) (HR) were investigated by low-temperature ashing prior to powder X-ray diffraction (LTA-XRD), X-ray fluorescence (XRF), inductively coupled plasma mass spectrometry (ICP-MS), and field emission scanning electron microscopy equipped with energy-dispersive X-ray analysis (FESEM-EDX). The results showed that the No. 2-1 coal is a low-medium ash yield (23%) and ultralow sulfur content (0.32%) meager coal. Minerals detected in this coal included clay minerals such as kaolinite, illite, and smectite, and non-clay minerals such as quartz, calcite, ankerite, tobelite, pyrite, and anatase. Compared with the Clarke values, selenium is unusually enriched (6.51 μg/g, CC = 130.20.), and arsenic is enriched (13.15 μg/g, CC = 7.31), while the content of other elements is normal: mercury (0.24 μg/g, CC = 2.40), vanadium (49.09 μg/g, CC = 0.36), chromium (38.77 μg/g, CC = 0.39), manganese (16.90 μg/g, CC = 0.02), lead (21.65 μg/g, CC = 1.73), cobalt (13.98 μg/g, CC = 0.56), nickel (22.76 μg/g, CC = 0.30), and ∑REE (96.20 μg/g, CC = 1.40). It is necessary to pay special attention to selenium and arsenic due to their potential impact on environment. By analyzing the trace element contents in vertical and adjacent layers, and the REE distribution patterns, we concluded that the coal seam has turned into a typical tectonically deformed coal due to the strong tectonic destruction and plastic deformation, yet we found no evidence that this could cause local enrichment or redistribution of the HR in the coal seam. The analysis of the correlation between the HR and ash yield, percentage of minerals, and main inorganic element content using FESEM-EDX showed that the majority of vanadium, chromium, lead, nickel, and REE mainly originate from kaolinite or illite, while mercury and selenium originate from pyrite.