Recently, the semiconductor and display industries have tried to reduce the emissions of perfluorocompounds (PFCs) from the globally environmental regulation. Total amount of PFC emission can be calculated from the flow rate and the partial pressures of PFCs. For the precise measurement of PFC emission amount, the mass flow controlled helium gas was continuously injected into the equipment of which scrubber efficiency is being measured. The partial pressures of PFCs and helium were accurately measured using a mass spectrometer in each sample extracted from inlet and outlet of the scrubber system. The flow rates are calculated from the partial pressures of helium and also, PFC destruction and removal efficiency (DRE) of the scrubber is calculated from the partial pressure of PFC and the flow rate. Under this method, the relative expanded uncertainties of the flow rate and the partial pressures of PFCs are ± 2% (k = 2) in case the concentrations of NF3 and SF6 are as low as 100 μmol/mol.