The impact of seismogenic ionosphere non-uniformity is considered on the Schumann resonance (SR) signals observed both in the vertical electric and two orthogonal horizontal magnetic field components. The model is able to interpret the anomalous signals observed in Japan in possible association with the earthquakes (EQs) in Taiwan. Changes in the SR intensity arise from a localized reduction of the ionosphere over the EQ epicentre. Signals in the regular Earth–ionosphere cavity are described by using the knee model of vertical conductivity profile. It is suggested that pre-seismic and seismic activity lowers the knee altitude by 20 km at the centre of disturbance, and the perturbation has the Gaussian radial dependence in the 1 Mm zone. The diffraction problem in the cavity with a localized disturbance is resolved by using the Stratton–Chu integral equation. The data of Optical Transient Detector are used to model the source distribution. A pronounced modification is obtained in the intensity around the fourth mode frequency in a form of abrupt spectral changes. The model data are found to be similar to observations, and properties of the model seismic anomalies are discussed.