Coagulation is an important process to remove organics from water. The molecular composition and structure of organic matter influence water quality in many ways, and the lack of information regarding the organics removed by different coagulants makes it challenging to optimize coagulation processes and ensure reclaimed water safety. In this paper, we investigated coagulation of secondary biological effluent from a municipal sewage treatment plant with different coagulants. We emphasized investigation of organics removal characteristics at the molecular level using Fourier transform-ion cyclotron resonance mass spectrometry (FT-ICR MS) coupled with electrospray ionization (ESI). We found that conventional coagulants can only partially remove condensed polycyclic aromatics and polyphenols with low H/C (H/C < 0.7) and highly unsaturated and phenolic compounds and aliphatic compounds with high O/C (O/C > 0.6). A new coagulant, CBHyC, had better removal efficiencies for all organics with different element compositions and molecular structures, especially organics that are resistant to conventional coagulants such as highly unsaturated and phenolic compounds and aliphatic compounds located in 0.3 < O/C < 0.8 and 1.0 < H/C < 2.0 regions and sulfur-containing compounds with higher O/C (e.g., anionic surfactants and their metabolites or coproducts). This study provides molecular insights into the organics removed by different coagulants and provides data supporting the possible optimization of advanced wastewater treatment processes.