Cell variations caused by the inevitable inconsistency during manufacture and use of battery cells have significant impacts on battery capacity, security and durability for battery energy storage systems. Thus, the battery equalization systems are essentially required to reduce variations of in-pack cells and increase battery pack capability. In order to protect all in-pack cells from damaging, estimate battery state and reduce variations, a system state estimation and energy optimal control framework for multicell lithium-ion battery system is proposed. The state-of-charge (SOC) values of all in-pack cells are firstly estimated using a dual-scale extended Kalman filtering (EKF) to improve estimation accuracy and reduce computation simultaneously. These estimated SOC values provide specific details of battery system, which cannot only be used to protect cells from over-charging/over-discharging, but also be employed to design state-feedback controller for battery equalization system. A two-stage hybrid state-feedback and output-feedback equalization algorithm is proposed. The state-feedback controller is firstly employed for coarse-grained adjustment to reduce equalization time cost with large current. However, due to the inevitable SOC estimation errors, the output-feedback controller is then used for fine-grained adjustment with trickle current. Experimental results show that the proposed framework can provide an effectively estimation and energy control for multicell battery systems. Finally, the implementation of the proposed method is further discussed for the real applications.