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 an operation of the microfluidic system, a rotator control block controlling a rotator, a position control block controlling the position of a moving unit, the moving unit moving to a position of the microfluidic structure, and a radiation energy source control block controlling energy of a radiation energy source, the radiation energy source using an electromagnetic wave to scan over a position of the microfluidic structure. Such a configuration allows effective control of a miniaturized portable microfluidic system.