The removal of small-molecular-weight organic matter (SMW-OM) is important for enhancing final water quality and increasing the performance of unit processes. However, the fate of SMW-OM during drinking water treatments has received a few concerns. In this study, the performances of three common processes (coagulation, adsorption, and ozonation) on treating SMW-OM were comprehensively studied at a molecular scale. For molecules only containing C, H, and O elements, coagulation favored the removal of unsaturated structures (low H/C) with oxygen-containing groups (high O/C). While for N-containing molecules, those with higher H/C were better removed. Adsorption preferentially removed reduced molecules (low O/C) and can remove molecules with a very low mass (20% removal rate for molecules with a mass of 300–350 Da). Therefore, it showed the best performance on decreasing the disinfection byproduct formation potential (DBPFP). Ozonation had a limited mineralization effect on organic contents. In addition, it transformed haloacetic acid (HAA) precursors to trihalomethane (THM) precursors by degrading aromatic structures to aliphatic compounds (e.g., aldehydes and ketones), and thus resulted in an increase in the THM formation potential. This study focused on the fate of SMW-OM in drinking water treatment and their DBPFP, illustrated its transformation process, and can provide guidance for enhanced drinking water treatment in practical applications.