Abstract: In this paper, the BLT equation is extended to calculate the shielding effectiveness (SE) of arbitrary observation points located in a double layer rectangular enclosure with an aperture on the basis of waveguide theory. Firstly, the surface containing an aperture of enclosure is equivalent to a two-port network, and the enclosure is equivalent to a rectangular waveguide shorted at each end. The signal flow graph can be built according to the equivalent model above. The aperture impedance is employed to calculate the scatter parameters of the two-port network, and the general BLT equation for SE of observation point on center line can be established. Then, the SE of arbitrary observation point can be obtained by using the waveguide theory. Finally, the results from our method are compared with that from CST simulation. The SE from our method reaches a good agreement with CST, and all the resonance frequencies are correctly predicted under 2.5 GHz. Our method takes less time and computer resource compared to CST, and it is helpful for analysis of resonance phenomenon and can easily get the influence of enclosure parameters.