The invention relates to a primary air pressure target value decision method and system based on the capacity of mill groups. The primary air pressure target value decision system is characterized in that an commissioning mill group counting module is used for counting up the number of current commissioning mill groups; a target value decision generating system logic module is used for judging whether the capacity of each of the current commissioning mill groups is within the allowable range of the average value, the target output value of the decision system is set as the average value of the capacity of the mill groups, and the capacity of primary air fans is controlled by a control system output module in combination with the output of a bias compensation logic module; when the target value decision generating system logic module judges that the capacity of any one of mills in the mill groups deviates from the allowable range of the average value, the primary operation of selecting the maximum value is performed on the deviation values of positive values, the maximum value is abandoned, the secondary operation of selecting the maximum value is performed, the value is recorded and accumulated with the average value to serve as the target output value of the decision system, a control output instruction is formed finally via the polygonal function in combination with the output of the bias compensation logic module, and the capacity of the primary air fans is controlled by the control system output module.