Axial wavelength is a key characteristic parameter of Taylor vortex flows. Thus, in the current study, the effect of Taylor vortex wavelength on the polymorphic nucleation and phase transformation of L-histidine was examined. The vortex wavelength was altered by altering the gap width between the outer and inner cylinders. Further, the vortex velocity was changed by controlling the inner cylinder rotation speed. Owing to the promotion of stable nucleation by the periodic fluid motion, the primary polymorphic fraction of the stable Form A of L-histidine in Taylor vortex flow [Couette–Taylor (CT) crystallizer] was much greater than that in a turbulent eddy flow [mixing tank (MT) crystallizer]. As the vortex wavelength decreased, stable nucleation was promoted, thus increasing the initial polymorphic fraction of the stable Form A. Moreover, the initial polymorphic fraction of the stable Form A increased as the vortex velocity increased. These experimental results are described based on molecular alignment effect of Taylor vortex on stable nucleation. The phase transformation of L-histidine was also strongly influenced by the vortex wavelength and vortex velocity. Hence, the rate of phase transformation in CT crystallizer was approximately ten-fold better than MT crystallizer.