The invention discloses a voltage balancing method and a voltage balancing system for a super capacitor module. The voltage balancing method comprises the steps of: acquiring voltages of all super capacitor single bodies in real time; determining the first super capacitor single body with the maximum voltage and the second super capacitor single body with the minimum voltage according to the voltages of all super capacitor single bodies in real time; judging whether a voltage difference between the first and second super capacitor single bodies is greater than a first voltage threshold value; if so, acquiring a present charging current or discharging current of the super capacitor module; judging whether the charging current is less than a charging current threshold value or whether the discharging current is less than a discharging current threshold value; and if so, carrying out voltage balancing treatment on the first and second super capacitor single bodies, so as to make an absolute value of the voltage difference between the first and second super capacitor single bodies after voltage balancing treatment less than a second voltage threshold value. The voltage balancing method and the voltage balancing system effectively reduce the difference between voltages of the super capacitor single bodies in the super capacitor module, avoid accident occurring in the using process of the super capacitor single bodies, make the super capacitor module operate within a reasonable and safe voltage range for a long time, and prolong the service life of the super capacitor module.