The invention discloses a stacked type three-order substrate integrated waveguide filter. The stacked type three-order substrate integrated waveguide filter comprises a top surface metal layer, a first dielectric substrate, a first middle metal layer, a second dielectric substrate, a second middle metal layer, a third dielectric substrate and a bottom surface metal layer which are stacked and distributed in sequence, wherein a first resonant cavity, a second resonant cavity and a third resonant cavity are formed in the first dielectric substrate, the second dielectric substrate and the third dielectric substrate respectively; an input port is formed in the top surface metal layer; an output port is formed in the bottom surface metal layer; the first middle metal layer is used for adjusting the magnetic coupling coefficient between the first resonant cavity and the second resonant cavity to obtain a first transmission zero point; and the second middle metal layer is used for adjusting the magnetic coupling coefficient between the second resonant cavity and the third resonant cavity to obtain a second transmission zero point. The stacked type three-order substrate integrated waveguide filter provided by the invention, by adjusting the electromagnetic coupling strength and obtaining extra transmission zero points, greatly improves frequency selection and harmonic suppression characteristics without changing the existing dimensions.