An airborne microbial measurement apparatus and a measurement method thereof are provided. An airborne microbial measurement apparatus according to an embodiment includes a discharge apparatus including a discharge electrode and a voltage supply unit applying a high voltage to the discharge electrode. A substrate is provided to a side of the discharge apparatus to collect an airborne microbe from air by a high voltage applied to the discharge electrode. A reagent injection apparatus supplies a dyeing reagent to the microbe collected on the substrate or a DNA of the microbe. A light emission measurement apparatus senses a quantity of light generated from the DNA to which the dyeing reagent is supplied. The discharge apparatus includes a controller controlling the voltage supply unit so that the voltage is applied to collect the airborne microbe or destroy an external wall of the collected airborne microbe.