The invention discloses a fair coordination control method and system based on electric quantity and reserve capacity. The method comprises the following steps: (1) calculating the total adjustment quantity of active power output of the whole network according to the area control deviation ACE, and calculating the distribution factor according to the total adjustment quantity; determining a plurality of units participating in the control within the AGC control period and the daily planned electric quantity completion degree of each unit; and (2) performing active power output distribution on aplurality of units participating in the control and issuing an adjustment instruction to the corresponding units until the total adjustment quantity distribution is completed according to the distribution factor and the daily planned electricity quantity completion degree of each unit. The mutually fair and reasonable instruction value can be greatly distributed to the units with different performances and different states by using the method and the system so as to avoid waste of power grid resources, loss of energy and damage to the units.