Oral chemotherapy is preferred but challenged by low bioavailability of anticancer drugs. Self-assembled nanoparticles are promising in solving this problem but the design of appropriate nanocarrier remains a difficulty. Here, using doxorubicin (DOX) as a drug model, the objective of this study was to illustrate how to design an efficient drug delivery system using molecular simulation and elucidate the influence of fatty glyceride chain length in hyaluronic acid (HA) copolymers on peroral absorption of DOX. The compatibility between DOX and HA-g-glyceryl monocaprylate (HGC), HA-g-glyceryl monolaurate (HGL) and HA-g-glyceryl monostearate (HGS) was assessed by molecular simulation using solubility parameters and Flory-Huggins interaction parameters (chi(FH)). Thereafter, HA copolymers were synthesized to verify the prediction. Among the copolymers, HGS showed the best compatibility with DOX followed by HGC and HGL. The physicochemical properties and stability of all the nanoparticles were copolymers structure dependent, with HGS-DOX nanoparticles showing the superior properties followed by HGC-DOX, HGL-DOX nanoparticles. The same order was found in cellular uptake, epithelial transport and in vivo absorption studies in rats, with HGS-DOX nanoparticles showing 7 times higher absorption after peroral administration than intravenous injection of DOX solution. In conclusion, molecular simulation is an effective strategy to the rational nanoparticle design for oral doxorubicin delivery.