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Daidzein is one of the most effective candidates for treating cardiovascular and cerebrovascular disease. However, considering its poor oral absorption and limited bioavailability, daidzein-loaded nanostructured lipid carriers-PLGA nanofibers were designed to handle the drawbacks. Daidzein-NLCs were successfully prepared by an emulsification and low-temperature solidification method. The physicochemical characteristics of NLCs were evaluated afterwards. Based on the preparation of daidzein-loaded NLCs, Daidzein-NLCs-nanofibers were optimized by electrospinning and were observed under Scanning Electron Microscope to capture the appearance. The sustained release profile of daidzein from Daidzein-NLCs-nanofibers in vivo was best fitted to the Kormeyer-Peppas equation. The in vitro skin permeable behavior showed the cumulative amount of daidzein from Daidzein-NLCs-nanofibers reached 21.71 μg cm−2 at 60 h, which was 3.78 times higher than pure daidzein solution. It demonstrated that the Daidzein-NLCs-nanofibers could significantly enhance the transported amount of drug. Confocal Laser Scanning Microscopy resulting images revealed a more effective content accumulation of Daidzein-NLCs-nanofibers than Daidzein-NLCs in epidermis. In vivo study indicated that Daidzein-NLCs-nanofibers had better skin retention than Daidzein-NLCs in the long term. The skin irritation experiment showed a positive result with no obvious stimulus observed. These results suggested that Daidzein-NLCs-nanofibers could be a potential candidate for transdermal delivery.