A charging balancing system and method thereof based on a battery operating process and are disclosed. This is done by detecting a state of all cells in a detecting battery assembly to generate detection parameters, analyzing the detection parameters to produce an operating process, selecting at least one of residual power estimation methods according to the operating process, so as to calculate a residual power of each cell, and adjusting the charging current and charging time for each cell according to the residual power. As such, the efficiency of charging balancing is promoted.