The present invention provides a controller of the erbium-doped optical amplifier based on double CPUs; the controller comprises a collocation module which is used for transmitting the controls parameters collocated by user to a main functional CPU module and outputting the calculation of the main functional CPU module; a main functional CPU module which is used for receiving the controls parameters from the collocation module and issuing the controls parameters and control algorithm to a calculation CPU module and realizing the auxiliary function of the erbium-doped amplifier; a calculation CPU module which is used for calculation with control algorithm according to the controls parameters and control algorithm issued by the main functional CPU module and the output of the erbium-doped amplifier provided by a detection control module and providing the calculation with the control algorithm to the detection control module; and a detection control module which is used for driving the erbium-doped amplifier by the calculation with the control algorithm and detecting the output of the erbium-doped amplifier and providing the detected output to the calculation CPU module. In this way,the flexibility of the system is promoted and the control function is greatly increased.