The hydrogen bonding interactions between methanesulfonic acid (MSA) and NHx compounds, such as ammonia (A), alkylamines (aNHx), and cyclic amino compounds (cNHx), were investigated using density functional theory, atoms in molecules, localized molecular orbitals-based energy decomposition analysis, and atmospheric clusters dynamic code methods. The results revealed that these dimers exhibit hydrogen bonds by SOH⋯N interactions. MSA–cNHx dimers showed higher binding energies compared to MSA–aNHx/A dimers. Topological analysis using AIM confirmed the presence of hydrogen bonding in these dimers by ρ(r) and ∇2ρ(r). The results of IRI indicate that there are different strength types of hydrogen bonding interactions in these dimers. LMO–EDA highlighted electrostatic interactions as the main attractive force, particularly in MSA–cNHx dimers. ACDC results showed a low evaporation rate for MSA–cNHx dimers compared to others. These findings suggest that MSA plays a crucial role in NPF events, and MSA–cNHx clusters could potentially act as nucleation nuclei in the atmosphere.