A control system that is reconfigurable during operation comprises a master controller which generates a bit stream, including reconfiguration information, according to the command of a user.The first slave controller comprises: a first dynamic reconfiguration module, which is a field programmable gate array (FPGA) reconfigured according to the reconfiguration information, and which calculates a control value; a static reconfiguration module which is an FPGA controlling the operation of a target apparatus according to the control value; and a control unit reconfiguring one or more of the first dynamic reconfiguration module and the static reconfiguration module according to the reconfiguration information.