An optimization method and system for a whole process of molecular-level oil refinery processing and a storage medium are described. According to an embodiment, for mixed products obtained by prediction from simulation of a molecular-level crude oil processing process, when physical properties of any mixed product do not meet any preset standard, or when a target parameter of the mixed products does not meet a preset condition, the proportion of different fractions entering respective petroleum processing device, an operating parameter in a product prediction model, and a mixing rule for mixing predicted products are adjusted, and the mixed products are re-obtained, until the product properties meet any preset standard and the target parameter meets the preset condition. Final predicted products are predicted by adjusting the proportion of fractions for secondary processing, and the production efficiency is improved by means of the simulation optimization of a production process.