In this paper, an observer based fault tolerant secondary control method is proposed to solve the problems of frequency restoration for active distribution network and state-of-charge(SoC) balance for energy storage systems(ESSs) under false data injection(FDI) attacks. Firstly, the secondary control model for frequency restoration and SoC balance of the active distribution network with ESSs under FDI attacks is formulated. Then, a state reconfiguration mechanism and an attack estimation observer are designed in the secondary control layer, and the exponential convergence of the observer is proved using the Lyapunov theory. To reduce the communication frequency between ESSs, a dynamic event triggered mechanism is introduced, and auxiliary observable variables are also introduced to update the states of neighbouring ESSs dynamically during triggering, and a parameter selection strategy is proposed to guarantee the system stability and exclude Zeno behavior. Finally, the effectiveness of proposed control strategy is verified by test in Matlab/Simulink.