An online adaptive balancing system is described in this paper. This system is mainly used for measuring and correcting imbalances of load adaptively in high throughput screening platform. Firstly, an online adaptive efficient balancing scheme for this system is proposed according to the characteristics of load of high throughput screening platform dynamic changes. Then, considering the system composition and structure, the method of the improved narrow band tracking filter and dynamic balance correction is proposed, meanwhile the adaptive control strategy is investigated. Finally, the experimental device is developed and the system is debugged to illustrate the effectiveness of the proposed method. The testing results show that the system of experimental device is feasible and valid.