Electrospinning has been considered a versatile and efficient method with low cost and ease of scalability for fabricating PVDF nanofibers. The binary hybrid solution of PVDF with different evaporation rates affecting the bending instability and the diversity of manufacturing parameters make it difficult to understand the evolution of molecular structure to reach the full potential of PVDF. In our work, the Taguchi design method was first used to investigate the influence of manufacturing parameters on fiber morphology and fiber diameter, which provided valuable insight in designing an electrospinning process for high-performance nanofiber materials. Based on analysis of orthogonal experiments, optimized PVDF nanofibers with similar diameters were produced by different preparation conditions to study the relationship between preparation conditions, molecular orientation of different crystalline phases and macroscopic property, which eliminates the influence of size effect on macroscopic properties. It was found that molecular orientation was determined by the competition between molecular chain stretching driven by electrostatic force and relaxation driven by gains in entropy. Rational control of the solvent ratio could balance this competition and lead to high tensile strength (16 MPa) and high β-phase percentage (76.3%). This work paves the way for fabricating high-performance fibers with designed morphologies for a variety of high-value, structure-based applications.