As the operating frequency increases, the accuracy of the measurement became more important. In recent years, there are various kinds of methods to solve the accuracy problem, one of them is to measure the relative permittivity of glass-epoxy printed circuit boards (PCB). This paper presents the new measurement environment of Electromagnetic Interfere (EMI) by the near-field scanning to find out the frequency. After getting the value of the frequency, relative permittivity can be calculated by the equation from cavity resonator. We show that the relative permittivity of a FR-4 sample decreases from 4.4 to 4.2 at the frequencies from 1GHz to 6GHz.