Natural organic matter (NOM) represents the major source of precursors for disinfection byproducts (DBPs), such as trihalomethanes (THMs) and haloacetic acids (HAAs), formed during disinfection of drinking water, but the molecular composition and reactivity of NOM remain not well understood. In this study, electrospray ionization coupled to Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) was used to characterize the molecular composition of NOM of 20 source waters taken across China for the purpose of determining the major precursors of THMs and HAAs at molecular level. It was found that there is a core of NOM compositions that are ubiquitous in different source waters, which is supposed to be more relevant for NOM quality. Formation potentials (FP) of THMs and HAAs were determined for NOM from different source waters during chlorination. Spearman's rank correlation was used to link THMFP and HAAFP with the individual molecular composition of NOM. Significant correlation (P < 0.001) was found between DBPFP and the NOM molecules with a high O/C ratio and low H/C ratio, indicating these molecules could contribute greatly to the formation of THMs and HAAs during chlorination. The link of THMFP and HAAFP with individual NOM molecules may allow us to develop more effective treatment strategies to achieve the drinking water safety objective: effective disinfection of waterborne pathogens while minimizing toxic DBPs.