This paper proposes a novel multi-layer substrate integrated waveguide (SIW) resonator loaded with asymmetric E-shaped slot-lines and shows a tri-band band-pass filter (BPF) using the proposed structure. In the previous literature, various SIW resonators have been proposed to simultaneously solve the problems of large area and high insertion loss. Although these SIWs have a lower insertion loss than planar-type resonators using a printed circuit board, the size of these structures tends to be larger. A multi-layer SIW resonator loaded with asymmetric E-shaped slot-lines can solve the above problems and realize a tri-band BPF without increasing the size to realize further miniaturization. The theoretical design method and the structural design are shown. Moreover, the configured structure is fabricated and measured for showing the validity of the design method in this paper.