Polymer‐based electrospun fibers have been intensively studied as antimicrobial membranes, drug carriers, and energetic materials. Inorganic fillers or small molecules have been routinely added into polymer matrices in order to enhance product functions. However, the electrospinning process is kinetically controlled and solvent rapidly evaporates due to the large surface‐to‐volume ratio of spinning liquid jet. When electrospinning a multicomponent system, complex phase behavior may occur and give rise to interesting internal structures of resulting products. Such kinetically driven phenomena deserve more attention for optimizing product performance. Here, electrospun poly(ε‐caprolactone)(PCL)/aminopropyl‐heptaisobutyl‐polyhedral oligomeric silsesquioxane (AMPOSS) fibers with AMPOSS content up to 30 wt% are studied as a model system to understand the impact of kinetically controlled phase separation on the fibers' internal structure, properties, and thermal stability. With sufficient AMPOSS loading, the hybrid fibers are found to have an AMPOSS‐shell/PCL‐core structure. The thermal stability of the as‐spun PCL/AMPOSS fibers is therefore greatly enhanced.