Electrospun core-shell fibers have great potentials in many areas, such as tissue engineering, drug delivery, and organic solar cells. Although many core-shell fibers have been prepared and studied, the morphology transformation of core-shell fibers have been rarely studied. In this work, the morphology evolution of electrospun core-shell polymer fibers driven by the Plateau-Rayleigh instability is investigated. Polystyrene/poly(methyl methacrylate) (PS/PMMA) core-shell fibers are first prepared by using blend solutions and a single axial electrospinning setup. After PS/PMMA core-shell fibers are annealed on a PS film, the fibers undulate and sink into the polymer film, forming core-shell hemispheres. The evolution process, which can be observed in situ by optical microscopy, is mainly driven by achieving lower surface and interfacial energies. The morphologies of the transformed structures can be confirmed by a selective removal technique, and polymer microbowls can be obtained.