Hydrated excess proton is ubiquitous in a wide range of systems within the fields of chemistry, biology, materials and engineering. Due to the strength of hydrogen bond between hydrated excess proton and water molecules, proton transport in aqueous environments is accompanied by change of molecular topology and breaking/forming of covalent bonds, which give rise to distinct behaviors of excess proton interacting with water. Therefore, we employed multiscale reactive molecular dynamics (MS-RMD) methods to understand excess protons in complex aqueous systems, which provides both an accurate description of topology change in PT and manageable computational cost. In this thesis, both ab intio molecular dynamics (AIMD) and MS-RMD were employed to understand the behaviors of hydrated excess protons in heterogeneous, complex aqueous systems, including: 1) water-vapor interface, 2) reverse-micellar interfaces and 3) protonated water clusters in acetonitrile. In the system of water-vapor interface, we primarily investigated the interfacial diffusion of excess proton, the surface affinity of the hydrated excess proton with two definitions of the interface: The Gibbs dividing interface (GDI) and the Willard-Chandler interface (WCI). The excess proton is found to exhibit a similar trend and quantitative free energy behavior in terms of its surface affinity as a function of the GDI or WCI. Importantly, the definitions of the two interfaces in terms of the excess proton charge defect are highly correlated and far from independent of one another, thus undermining the argument that one interface is superior to the other when describing the proton interface affinity. Regarding the reverse micelles system, slow proton transport was observed which becomes faster with increasing micellar size. Further analysis reveals that the slow diffusion of an excess proton is a combined result of slow water diffusion and the low proton hopping rate. This study also confirms that a low proton hopping rate in reverse micelles stems from the interfacial solvation of hydrated excess protons and the immobilization of interfacial water. The low water density in the interfacial region makes it difficult to form a complete hydrogen bond network near the hydrated excess proton, and therefore locks in the orientation of hydrated proton cations. The immobilization of the interfacial water also slows the relaxation of the overall hydrogen bond network. Finally, multiple species of protonated water clusters were identified in acetonitrile, with the primary cluster species being an H9O4+ Eigen cation, followed by a three-water H7O3+ cation. Further analysis of the structural properties and special pair anisotropy decay trends identifies the H7O3+ cluster as an Eigen cation with an acetonitrile replacing one of the solvating water molecules, not a Zundel cation with an additional water molecule as has been previously suggested. The overall Eigen-like nature of the protonated water clusters was found to be the result of the localization of the excessive charge defects. We conclude that an acetonitrile-acid-based water system contains multiple species of Eigen-like protonated water clusters