Magnetic-field-assisted electrospinning (MFAES) is a simple and effective method to align polymer nanofibers. In this method, further research is needed to identify alignment mechanism. Hence, this article includes statistical analysis of affecting factors to investigate alignment mechanism in MFAES. Tip to target distance, magnets distance, voltage, and collection time, which are recognized as the most effective factors on nanofibers alignment, were applied in design of experiments. Central composite method was applied to get required experiments with designed expert 8 software. A response surface was proposed with regression coefficient of 97%. Then, the common physics concepts and statistical results were used to discuss the affecting mechanism of the electric and magnetic fields on the electrospinnig jet and the nanofibers alignment. Field emission scanning electron microscopy images were used to characterize the nanofibers alignment and calculate overall alignment percentage using a proposed statistical combinatorial weighted percentage formula. MFAES method, used in this research, achieved 95.3% polyacrylonitrile-aligned nanofibers. © 2014 Wiley Periodicals, Inc. J. Appl. Polym. Sci. 2014, 131, 41179.