A plant controlling system includes: a velocity-type PID controlling unit to receive a control deviation between a process value and control set value, and calculate and output a manipulated variable deviation for operation targets; a switching unit to switch and then output the manipulated variable deviation from the velocity-type PID controlling unit to the operation targets; manual operating units, having an integration function, that are associated with the operation targets and output either one of the manipulated variable calculated by the integration of the manipulated variable deviation output from the switching unit and a manipulated variable based on a manually set value to the respective associated operation targets based on a control mode of the operation targets; and a switch controlling unit configured to control operation of the switching unit based on the control mode of the operation targets and the manipulated variables output to the operation targets.