For materials containing fluorine, it has been generally accepted that fluorinated segments or end groups tend to aggregate in the outer surface because of the low surface energy, which endows the fluorinated materials with special surface properties such as self-cleaning, superhydrophobicity, and so forth. However, for the electrospun fibrous membranes of polyurethane elastomers containing perfluoropolyether segments (FPU), abnormal fluorine aggregations in the core of the electrospun fibers were observed. The XPS analysis indicated a rather low fluorine content at the surface of the electrospun FPU fibers. Further study with dynamic light scattering and fluorescence showed that FPU chains can form aggregates in the concentrated solution. Therefore, it can be deduced that the rapid evaporation of solvent and fast formation of fibers during the electrospinning process could result in the freeze-in of the aggregated chain conformation and the depletion of fluorine units on the surface of the electrospun FPU fibers.