A calculation method based on BLT equation is proposed for analyzing the shielding effectiveness of enclosures containing apertures. This method can accurately and quickly obtain the shielding effectiveness of oblique incidence and polarization, off-centered apertures, and multi-apertures in two walls of enclosures. Aperture scattering matrix can be obtained according to equivalent circuit theory. Then, propagation relationships and reflection relationships are established, and finally the general BLT equation is derived, including the coupling to apertures. In order to verify the validity, the results are compared with these from equivalent circuit theory and CST. With the same aperture impedance, the aperture scattering matrix contains the interaction of the electromagnetic field so that the method proposed in this paper owns higher precision and can predict more resonant modes compared with the equivalent circuit theory. This method takes less time and computer resource compared with CST which cannot easily get the influence of enclosure parameters.