Solvent extraction has been ubiquitously used to recover valuable metals from wastes such as spent batteries and electrical boards. With increasing demands for energy transition, there is a critical need to improve the recycling rate of critical metals, including copper. Therefore, the sustainability of reagents is critical for the overall sustainability of the process. Yet, the recycling process relies on functional organic compounds based on the hydroxyoxime group. To date, hydroxyoxime extractants have been produced from petrol-based chemical feedstocks. Recently, natural-based cardanol has been used to produce an alternative hydroxyoxime. The natural-based oxime has been employed to recover valuable metals (Ga, Ni, Co) via a liquid/liquid extraction process. The natural compound has a distinctive structure with 15 carbons in the alkyl tail. In contrast, petrol-based hydroxyoximes have only 12 or fewer carbons. However, the molecular advantages of this natural-based compound over the current petrol-based ones remain unclear. In this study, molecular dynamics simulation was employed to investigate the effect of extractant hydrocarbon chains on the extraction of copper ions. Two hydroxyoxime extractants with 12 and 15 carbons in the alkyl chain were found to have similar interactions with Cu2+ions. Yet, a slight molecular binding increase was observed when the carbon chain was increased. In addition, lengthening the carbon chain made the extracting stage easier and the stripping stage harder. The binding would result in a lower pH in the extraction step and a lower pH in the stripping step. The insights from this molecular study would help design the extraction circuit using natural-based hydroxyoxime extractants. A successful application of cashew-based cardanol will improve the environmental benefits of the recycling process. With cashew-producing regions in developing countries, the application also improves these regions’ social and economic sustainability.