Computer aided molecular design (CAMD) has been used widely for solvent design. It is a reverse approach in the selection of solvents for real application. CAMD is suitable for ionic liquid solvent design due the vast possibilities of ionic liquid molecular structures to be identified. Ionic liquid has broad ranges of applications especially in separation especially in carbon capture and azeotropic separation. This is due to the unique structures of ionic liquid that can be tailored for specific product separation. This study focuses on ionic liquid design framework for phytochemical extraction, incorporating the prediction of the extraction yield using the microwave-assisted method. The framework was developed in several stages. Stage 1 identifies the user needs, problems and constraints as well as target properties. Stage 2 comprise of comprehensive database development for ionic liquid and phytochemical properties; while property models library was developed in Stage 3. Stage 4 involved the development of solvent design algorithm for ionic liquid selection for the targeted process. In Stage 5, depending on the type of extraction method considered, either using normal Soxhlet or a microwave-assisted extraction, the extraction yield can be predicted using the process performance model. The performance model for the liquid extraction is the thermodynamic solid-liquid equilibria model while for the advanced extraction method, the model was obtained through optimization of the experimental extraction process. This systematic framework is illustrated through a case study involving flavonoid and phenolic acid extraction from Ortosiphon aureus. Based on the yield prediction, 1-ethyl-3-propylimidazoilum bromide can extract 29.92 mg/g and was selected as a solvent for Flavonoid extraction using Microwave-assisted extraction. The design framework is able to find the optimal ionic liquid candidate for the extraction process.