Provided are an apparatus and a method of controlling a microfluidic system, and the microfluidic system. The apparatus of controlling the microfluidic system includes a central control block controlling the overall operation of the microfluidic system, a rotator control block controlling a rotator in response to a first control signal, the rotator rotating the rotary body of the central control block and causing a fluid sample to flow due to a centrifugal force generated by the rotation of the rotary body, a position control block controlling the position of a moving unit in response to a second control signal of the central control block, the moving unit moving to a predetermined position of the microfluidic structure, and a radiation energy source control block controlling energy of a radiation energy source in response to a third control signal of the central control block, the radiation energy source using an electromagnetic wave to scan over a predetermined position of the microfluidic structure. Such a configuration allows effective control of a miniaturized portable microfluidic system.