A lignite monomer of organic oxygen (LMO) and a lignite monomer of organic nitrogen (LMN) were constructed based on the occurrence forms of organic oxygen/nitrogen in lignites, then their intermolecular hydrogen bonding interactions (HBIs) with water molecules were investigated using the density functional theory (DFT) and the quantum theory of atoms in molecules (AIM). The results show that a variety of LMO-(H2O) (n = 1-16) and LMN-(H2O)(n) (n = 1-12) complexes were formed. A water cage cluster containing 16 water molecules and a water film cluster containing 10 water molecules were observed in LMO-(H2O)(16) and LMN-(H2O)(12) complexes, respectively, and cyclic water tetramers were the dominated existing form of water clusters. The ratio of hydrogen bonding energy (HBE) among water molecules to the total HBE in lignite water complexes gradually increases with the number of water molecules increasing, and the ratios are 84% and 44% in LMO-(H2O)(16) and LMN-(H2O)(12) complexes, respectively. The intermolecular HBIs in LMO-(H2O)(12) and LMN-(H2O)(12) complexes can be divided into purely weak and medium closed-shell non-covalent interactions. Molecular electrostatic potential analyses imply that the most formation sites of hydrogen bonds are transferred to the O atoms of water molecules from the O and N atoms in LMO and LMN with the number of water molecules increasing in LMO-(H2O)(n), and LMN-(H2O)(n) complexes.