Agitation plays an important role in the hyaluronic acid (HA) fermentation process. However, views about the effect of agitation on HA production remain controversial. We investigated the effect of agitation on cell growth and HA synthesis during HA fermentation process by using Computational Fluid Dynamics (CFD) technology. The results showed that the biomass and HA yield changed a little with the increase of impeller speed, but the HA molecular weight firstly increased and then decreased. The results of phase agitation control strategy demonstrated that the influence of agitation on the HA molecular weight mainly exhibited at the stage of HA synthesis. Moreover, the CFD simulation results indicated that when impeller speed increased, the mixing time reduced while the shear rate increased significantly. The removal of anchor could moderate the contradiction between the mixing time and shear rate, and finally the HA molecular weight increased by 23.9%. The results of this work could provide guidelines for optimizing the HA fermentation, as well as the bioreactor design and scaling up.