The traditional van Krevelen diagram, the nominal oxidation of organic carbon, and several aromaticity indexes generally considered C, H, O, N, P, and S factors, or just C, H, and O. However, these evaluated methods may provide incorrect interpretation for high-resolution mass data of organics containing halogen elements. Therefore, we adapted the van Krevelen diagram and the other indexes with halogen elements and verified with 2235 model organics. The results demonstrated that the modified van Krevelen diagram and the adjusted indexes were more accurate for the analysis of mass data, either in the compound classification or in the evaluation of oxidation state of organic matter.