In this study, the multiple nested state‐of‐the‐art Weather Research and Forecasting (WRF) model is used to investigate the impact of the subgrid‐scale (SGS) vertical turbulent mixing parametrization on hurricane eyewall asymmetric structures and the formation of eyewall mesovortices. Hurricane Isabel (2003) was simulated by a series of numerical experiments with different SGS vertical turbulent mixing parametrizations including the Yonsei University, Mellor–Yamada–Janjic, Mellor–Yamada–Nakanishi–Niino 2.5 level and Mellor–Yamada–Nakanishi–Niino 3 level schemes. The simulations show that the vertical turbulent mixing scheme not only substantially affects the SGS vertical transport of heat and moisture but also has an important bearing on the storm axisymmetric structure, eyewall mesovortices and other resolved asymmetric features in the vicinity of the hurricane eyewall. The analyses show that the vertical turbulent mixing processes provide a mechanism to affect the barotropic instability for generation of eyewall mesovortices through changing the vortex basic state potential vorticity (PV) field and generating eyewall disturbances with different frequencies. Our numerical experiments show for given external conditions that the magnitude and vertical distribution of the eddy exchange coefficients are the key factors that regulate the characteristics of eyewall disturbances. Such a modulation of eyewall structure by the eddy exchange coefficients is realized through the complicated interaction among SGS vertical turbulent mixing, mesoscale structures, diabatic heating and barotropic instability.