An air cleaning system and a method of controlling the same, the air cleaning system including a particle separation device for suctioning indoor air to separate microbial particles from air particles, a collection device collecting the microbial particles separated by the particle separation device, a luminescence measurement device for detecting an amount or intensity of light emitted from the microbial particles collected in the collection device, and at least one air cleaning device that selectively operates on the basis of contamination of the microbial particles detected by the luminescence measurement device.