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Structural nanocomposites that provide fast dissolving drug release profiles are highly in demand in pharmaceutics. In this study, a poorly water-soluble drug such as quercetin or tamoxifen citrate (TC) was selected as a model active pharmaceutical ingredient. Core-shell nanofibers with ultra-thin shells were designed and prepared using modified coaxial electrospinning. Polyvinylpyrrolidone (PVP) K90 or Polycaprolactone (PCL) was selected as core. The drugs and PVP K10 were selected as shell. All types of solutions can be used as the shell fluids in modified coaxial process regardless of their electrospinnability, which means the increasing functional ingredients and unspinnable matrix can be processed. Evaluations via SEM and TEM demonstrated that the core-shell nanofibers had linear morphology with a shell thickness smaller than 100 nm. XRD and FTIR results showed that the model drug was distributed in the polymeric matrix amorphously and that PVP K10 had good compatibility with quercetin or TC. In vitro dissolution tests suggested that the core-shell nanofibers with ultra-thin shells released the loaded cargoes in the dissolution media within 1 min. The present investigation paved a new way for implementing the modified coaxial processes, which can be utilized to fabricate structural nanocomposites with ultra-thin shells for enhancing the fast dissolution of poorly water-soluble drugs.