A new integrated sustainable solvent and process design framework is proposed based on GDP (generalized disjunctive programming) to separate the naphthenic and aromatic components from naphtha. First, the detailed molecular composition information of naphtha is obtained using a molecular reconstruction model based on feasible bulk properties. Two group-based virtual molecules are then presented to express naphtha components for the liquid–liquid extraction process design. Second, four separation performance indicators and eight SHE (safety, health and environment) metrics are screened and described for the sustainable solvent design on the basis of the UNIFAC model and functional groups. The solvent structures are modelled through the improvement of the octet rule. Last, a conceptual liquid–liquid extraction process is proposed and expressed as a CAMPD (computer aided molecular and process design) optimization problem combining with the rigorous process mechanism model, sustainable solvent design model and molecular information model of naphtha. Especially, GDP is tailored to express the discrete choices in the simultaneous optimization design of solvents and processes and address the challenge of the large-scale framework solution. Compared with the process using the traditional solvent sulfolane, the content of the separated naphthenic and aromatic components is improved by 10.37%. At the same time, the sustainability is enhanced according to SHE assessment.