1,3-Propanediol (1,3-PDO) holds significant industrial importance, but its eco-friendly extraction remains a challenge. To address this, we investigated the performance of four ionic liquidsand [Bmim][TFO]) via Molecular Dynamics simulations for 1,3-PDO extraction. Analysis of radial distribution functions (RDF) and spatial distribution functions (SDF) demonstrated enhanced 1,3-PDO coordination around [Bmim][SCN], with higher density in [Bmim][SCN] and [Bmim][TFO] compared to [Bmim][NPF2] and [Bmim][NTF2]. [Bmim][TFO] and [Bmim][SCN] exhibited pronounced RDF anion peaks, indicating robust hydrogen bonding interactions and a higher concentration of 1,3-PDO around them. [Bmim][SCN] formed the highest number of hydrogen bonds (1.639) due to its coordinating [SCN]-anion, which bonded with 1,3-propanediol's [OH]-groups. In contrast, non-coordinating anions in [Bmim][NPF2] and [Bmim][NTF2] formed fewer hydrogen bonds. Within a ternary system, [Bmim][SCN] and [Bmim][TFO] excelled at 1,3-PDO extraction, surpassing [Bmim][NPF2] and [Bmim][NTF2] with selectivity around 29. Anion variations significantly influenced distribution coefficients and selectivity values. COSMO-SAC, a predictive thermodynamic model, confirmed 1,3-PDO's strong interaction with [Bmim][SCN] and [Bmim][TFO]. This study enhances our understanding of IL-1,3-PDO systems and their potential in eco-friendly extraction processes. [Bmim][SCN] emerges as the most promising ionic liquid, offering insights into anion selection's role in shaping ionic liquid properties for 1,3-PDO extraction.