The invention discloses a universal variable operation controller for variable operation such as farmland seeding, fertilizing and pesticide spraying and a control method of the universal variable operation controller. The universal variable operation controller is matched with a corresponding sensor and a corresponding executing mechanism and can be used for controlling the variable operation of air suction seeding, outer groove-wheel type fertilizing and spray boom type pesticide spraying and simultaneously controlling the running speed of a wheel type agricultural machine, and a stable running speed is provided for the variable operation. The universal variable operation controller is formed by an ARM (Advanced RISC Machines)-9 core unit, a power supply module, a pushing rod driving module, an electromagnetic valve control module, a motor control module, a voltage output module, a pulse signal conditioning module, a current measuring module and a voltage measuring module. The control method comprises the steps of inquiring a prescription map to obtain prescription information of a farmland in a position according to the position where an agricultural implement is located, and calculating to obtain a target application amount. By adopting an appropriate algorithm, the variable operation control is realized, meanwhile, the agricultural machine is controlled to run at a stable setting speed through an accelerator pedal, and the accuracy of variable operation is increased.