The species, distribution and occurrence of harmful substances in coal and their influences on the environment have been systematically reviewed. The shape of pyrite in coal, formation generations, the textures of organic sulfur, and the geological genesis of sulfur in coal have been probed into as well. Three formation generations of pyrite in coal can be divided according to the δ³⁴C values. The contents of thiophene in coal increase with coal rank. The contents of organic sulfur in coal depends on coal macerals. The sources of sulfur in coal mainly come from coal-forming plants and sedimentary environments, and the latter is more important. The δ³⁴C value of sulfur from sea water prefers to be negative, however it prefers to be positive if the sulfur comes from fresh water. The species, distribution, occurrence and accumulation of hazardous minor and trace elements in coal and their harmful influences on the environment have been expounded. The contents and species of minor and trace elements in coal not only depend on the depositional environments and macerals, but also on the regional geological setting. The distribution and occurrence of minor and trace elements in coal can be determined with direct and indirect methods. The minor and trace elements in coals mainly originated from paleosoil, source materials, sea water, magmatic hydrothermal solution and underground water. The components of polycyclic aromatic hydrocarbons in coal, occurrence, and their impact on the environment as well on human health have been detailedly discussed too. The contents of PAHs in coal mainly depends on coal rank and sedimentary environments. However, the species and contents of PAHs in products of coal combustion are different from coal. The impact of particulate matter on the human health is related with the grain size of soot from coal combustion. The smaller is the grain size, the more hazardous is. The PAHs resulted in cancer and mutation is mainly from particulate matter of soot. The PAHs in air mainly come from coal combustion. Finally the existing problems and development trend for the study of harmful substances in coal are pointed out. The coal geology, geochemistry and environmental sciences should be systematically considered during study the harmful substances in coal. And the environmental pollution evaluation of harmful substances should be organically related with environmental pollution remediation as well.