The invention relates to a multifunctional control system and a control method of a battery used in a substation, which is characterized in that the multifunctional control system comprises a currentacquisition module, an input end of the current acquisition module is connected with a current sensor, and an output end is connected with an input end of an A/D converter. The input end of the temperature acquisition module is connected with the temperature sensor, and the output end is connected with the input end of the A/D converter. The output of A/D converter is connected with CPU through I/O interface. The CPU is also connected with human-computer interaction module, discharge load and voltage balancing module through I/O interface, and the discharge load and voltage balancing module are electrically connected with each single battery respectively. The control method comprises the following steps of: balancing control of a battery pack; SOC estimation of battery pack; measurement ofinternal resistance of battery pack.