Sugar-based byproducts such as molasses and bagasse are abundant resources for large-scale biobutanol commercialization. This study presents a comprehensive kinetic model to analyze ABE (acetone-butanol-ethanol) fermentation by C. saccharoperbutilacetonicum N1-4, emphasizing diverse carbon sources and furaldehyde co-utilization. By leveraging sensitivity analysis against models in the literature and the proposed model as well as parameter optimization using Scilab®, the potential for the simultaneous utilization of sugarcane molasses and bagasse-derived sugars alongside furfural and HMF for butanol synthesis was assessed. These findings revealed that despite the microbial preference for hexose sugars, the incorporation of up to 25% pentose sugars did not significantly hinder butanol production. However, furaldehydes perturbed butyric acid assimilation and acetyl-CoA consumption while enhancing acetone-butanol-ethanol synthesis. The simulation highlighted the peak concentrations of furfural and HMF (0.33 mmol L−1 and 0.03 mmol L−1, respectively), underscoring their conversion to less toxic alcohols, thereby augmenting metabolism. Sensitivity analysis underscores the necessity of enhancing butyric acid assimilation, providing critical insights for optimizing ABE fermentation and advancing biobutanol production from sugar-based byproducts.