The invention relates to a coupling folding substrate integrated waveguide filter, comprising a first metal layer, a first dielectric substrate layer, a second metal layer, a second dielectric substrate layer and a third metal layer, which are longitudinally stacked; the first dielectric substrate layer, the second metal layer and the second dielectric substrate layer are provided with a pluralityof vertically penetrating metal via holes that are arranged in a U shape, and the first dielectric substrate layer and the second dielectric substrate layer are provided with transverse I-shaped distributed metal via holes in the opposite side of a U-shaped opening. A first gap perpendicular to the U-shaped bottom is formed in the U-shaped via hole of the second metal layer, a second gap is formed between one side edge of the second metal layer and the transverse I-shaped via holes of the first and second dielectric substrate layers, the first gap and the second gap realize cross coupling ofthe resonant cavity and energy coupling of the upper layer and the lower layer, and the position of a filter transmission zero on the left side and the right side of a pass band is adjusted by adjusting the length of the first gap. The filter in the invention adopts the folding integrated waveguide resonant cavity with a double-layer coupling structure to realize miniaturization of the filter; andthe position of the filter transmission zero is controllable by introducing and adjusting the cross-coupling structure.