Fucoxanthin (Fx) has poor water solubility and bioavailability, which limits its application in the food industry. To improve the physicochemical properties of Fx, hydroxypropyl-β-cyclodextrin (HP-β-CD) encapsulated Fx nanofibers (Fx/HP-β-CD nanofibers) were fabricated via electrospinning without using polymer. Molecular docking analysis showed the Fx/HP-β-CD nanofibers contained Fx and HP-β-CD at 1:2. Morphological analysis revealed the nanofibers were homogeneous without beads, having a diameter around 499 nm. The thermostability of Fx was significantly improved after encapsulationg by HP-β-CD. Animal studies showed that there was a 14% decrease of body weight, 11% white adipose tissue reduction and 9% lower of liver triglyceride for the mice treated with Fx/HP-β-CD nanofibers as compared with that of Fx treated mice. The total cholesterol was reduced by 23% in mice serum after treatment with Fx/HP-β-CD as compared with that of Fx. Interestingly, the Fx/HP-β-CD in this study could attenuate the testicular histopathology in obese mice.