In this study, molecular simulation was used to explore the structural characteristics and water transport performance of Amphotericin B-Brgosterol (AmBEr) channels. A molecular dynamics (MD) technique was used to construct two types of molecular models of AmBEr channels: single-layer channel (SLC) and double-layer channel (DLC). A MD simulation was used to illustrate the differences between SLC and DLC AmBEr models with respect to structure, channel diameter, interior affinity, and transportation behavior of water molecules. A Monte Carlo (MC) method was adopted to investigate the sorption behavior in these two types of AmBEr channels. The intramolecular properties and intermolecular interactions indicated the feasibility of the simple model construction method adopted in this study. The internal diameter and channel shape showed that the use of funnel-type AmBEr channels would lead to high levels of permeability and selectivity. The special tunnel shape was reflected in the diffusion calculation that resulted in a high displacement of water molecules in two types of channel models. The water molecule-channel hydrogen bond distribution and snapshot analyses of the adsorption site revealed an affinity between the amphotericin B monomer and water molecules. The novel chemical structure of the amphotericin B monomer features simultaneous hydrophilic and hydrophobic segments. This particular structural characteristic was reflected in the unique shape of the water adsorption isotherm curves, which show a unique three-step increase in equilibrated water pressure. In transport prediction, two AmBEr models had similar permeability values but different water transport mechanisms. Concisely, fabrication of the artificial water channel would help to enhance the water permeability in the water transport process. The results from the simulation provided valuable information for structural characterization and in estimating the transport behavior of the molecules in the AmBEr channels.