In tissue engineering research, there has recently been considerable interest in using electrospun biomimetic nanofibers of hybrids, in particular, from natural and synthetic polymers for engineering different tissues. However, phase separation between a pair of much dissimilar polymers might give rise to detrimental influences on both the electrospinning process and the resultant fiber performance. A representative natural-synthetic hybrid of gelatin (GT) and polycaprolactone (PCL) (50:50) was employed to study the phase separation behavior in electrospinning of the GT/PCL composite fibers. Using trifluoroethanol (TFE) as the cosolvent of the two polymers, observation of visible sedimentation and flocculation from dynamic light scattering analysis of the GT/PCL/TFE mixture both showed that phase separation does occur in just a few hours. This consequently led to gradually deteriorated fiber morphologies (e.g., splash, fiber bonding, and varied fiber size) over time during electrospinning GT/PCL. Quantitative analysis also indicated that the ratio of GT to PCL in the resultant GT/PCL fibers was altered over time. To address the phase separation related issues, a tiny amount (<0.3%) of acetic acid was introduced to improve the miscibility, which enabled the originally turbid solution to become clear immediately and to be single-phase stable for more than 1 week. Nanofibers thus obtained also appeared to be thinner, smooth, and homogeneous with enhanced performance in wettability and mechanical properties. Given the versatility and widely uses of the electrospun GT/PCL and other similar natural-synthetic hybrid systems in constructing tissue-engineered scaffolds, this work may offer a facile and effective approach to achieve finer and compositionally homogeneous hybrid nanofibers for effective applications.