A systematic multiscale method is presented for studying the structure performance relationship of drug-delivery systems (DDSs). The objective is to provide direction and guidelines toward the design and development of novel DDSs. Atomic simulation methods are used to evaluate the interactions between each pair of components in a DDS, from which the compatibility between drug and carriers can be well-predicted. Mesoscale simulation is applied to investigate the mesostructures of DDSs, from which the performances of products can be predicted. Finally, the drug-loaded nanoparticles can be prepared and evaluated through experiments involving loading efficiency, drug-release behaviors, and so on. The hydrophobic drugs doxorubicin and paclitaxel were considered as examples. The multiscale approach was used to investigate the structure-performance relationship of DDSs for these two drugs. All of the experimental results agreed well with the simulation results, indicating that the systematic multiscale method can provide a powerful tool for designing and developing DDSs.