A fundamental understanding of the structural heterogeneity and optical properties of ionic liquids is crucial for their potential applications in catalysis, optical measurement, and solar cells. Herein, a synergistic approach combining molecular dynamics simulations, excited-state calculations, and statistical analysis was used to explore the explicit correlation between the structural and optical properties of one imidazolium amino acid based ionic liquid, 1-butyl-3-methylimidazolium glycine. The estimated absorption spectrum successfully rationalizes the unusual and non-negligible absorption band beyond 300 nm for the neat imidazolium-based ionic liquid. The absorption behavior of imidazolium-based ionic liquids is shown to be sensitive to the details of their locally heterogeneous environments. We quantitatively highlight the imidazolium moiety and its various molecular aggregations, rather than the monomeric imidazolium moiety, that are responsible for the absorption characteristics. These results would improve our understanding of the preliminary interplay between structural heterogeneity and optical properties for neat imidazolium-based ionic liquids.