Spectral Resonance Structures (SRS) of Ionospheric Alfven Resonator (IAR) are investigated by analysing the magnetic field data of a high sampling frequency induction coil magnetometer, installed at a low latitude Indian station, Shillong$$(25.56^\circ N, 91.86^\circ E, dipole L=1.08 )$$ ( 25 . 56 ∘ N , 91 . 86 ∘ E , d i p o l e L = 1.08 ) . One of the distinguishing features of IAR resonance structure observed at this latitude is the excitation of two spectral resonance structures simultaneously, one with a small frequency separation and the other with a large frequency separation of subsequent harmonics. The seasonal variation shows that the occurrence of double SRS is more favoured during winter, where, out of the total IAR events observed during winter, about $$47\%$$ 47 % show clear signatures of double SRS and no double SRS are observed during summer. We have examined the altitudinal variation of refractive index using IRI 2016 model to understand the role of local ionospheric conditions in the formation of double spectral resonance structures. Our study reveals that the excitation of double SRS is related to the E-region to F-region variability of refractive index of the ionosphere. We also report that the double spectral resonance structures at Shillong are always observed only in the $${B}_{x}$$ B x component of the magnetic field variation. Graphical Abstract
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