Recently, traditional solvent-based polyurethanes have increasingly been replaced with waterborne polyurethanes (WPUs) to adopt greener synthesis methods that avoid VOCs emissions. In the synthesis of WPUs, where polymerization occurs in water, the role of emulsifiers that enable the dispersion of polyurethane is a crucial factor that determines the properties and functionality of WPUs. This study employed both experimental and computational simulation approaches to investigate the effect of the chemical structure and concentration of internal emulsifiers on the dispersibility and physical properties of anionic WPUs. As the concentration of internal emulsifiers increased, the hydrophilicity and breathability of the WPUs films improved, while water resistance declined. However, higher emulsifier concentrations led to reduced thermal stability, lower elongation at break, and decreased molecular weight of the films. Unlike dimethylolpropionic acid (DMPA), dimethylolbutanoic acid (DMBA) enabled the formation of stable polymer dispersions with smaller particle sizes at lower concentrations and facilitated the production of less hydrophilic films. Dissipative particle dynamics simulations revealed that WPUs utilizing DMPA dispersed more uniformly in water than those using DMBA.