Nowadays still widely used manual filling control approach to the small-doses and high-speed liquid medicine filling system with high filling accuracy requirement is difficult to reduce filling errors due to dynamic behavior time-varying of the high-speed filling system (HSFS). In order to improve the filling control accuracy of the HSFS, this paper designs an intelligent filling controller (IC) based on the model of the HSFS. On the basis of the IC, for solving the problem caused by filling behavior nonlinearity, this paper proposes an adaptive intelligent filling control method, in which a locally linear model of the HSFS is built online by the least squares method (LSM), the sensitivity of the filling system is analyzed online based on the model, and an adaptive controller is designed to overcome the influence of dynamics time-varying and nonlinearity of the HSFS. Real-time filling control experiments are carried out using manual control, the intelligent control and the adaptive control methods, respectively. The results show that the adaptive control performance is the best compared to other two control approaches, both the intelligent controller and adaptive controller can cope with the behavior time-varying of the HSFS very well, and the adaptive controller has the ability to overcome the influence of nonlinearity of the HSFS.