Daidzein (DZ) is an ideal Chinese herb for treating cardiocerebrovascular disease. Despite its poor water solubility and limited application, DZ was successfully loaded, along with penetration enhancer azone, onto core-shell-type polymer-lipid nanoparticles through a two-step preparation method. The mean particle diameter, encapsulation efficiency, and drug-loading rate of DZ-polymer-azone-lipid nanoparticles (D-P-Azone-LNs) were 77.59 ± 2.26 nm, 79.91% ± 1.46%, and 1.50% ± 0.02%, respectively. In skin penetration experiment, the cumulative amount of DZ from D-P-Azone-LN reached 14.91 μg•cm −2 at 72 h. This amount was 1.44 and 6.01 times higher than those of DZ-polymer-lipid nanoparticles (D-P-LNs) and DZ solution, respectively. Confocal laser scanning microscopy was used to conduct a qualitative analysis. In vivo study, D-P-Azone-LN achieved better skin retention than those of D-P-LN and DZ. Furthermore, no significant irritation was observed in the skin irritation experiment. These results suggested that the core-shell polymer-lipid nanoparticles, which combined the properties of polymer and lipid nanoparticles, can offer a useful formulation for enhancing the skin permeation of drug for transdermal delivery.