Resonance is instrumental in modern optics and photonics for novel phenomena such as cavity quantum electrodynamics and electric-field-induced transparency. While one can use numerical simulations to sweep geometric and material parameters of optical structures, these simulations usually require considerably long calculation time (spanning from several hours to several weeks) and substantial computational resources. Such requirements significantly limit their applicability in understanding and inverse designing structures with desired resonance performances. Recently, the introduction of artificial intelligence allows for faster predictions of resonance with less demanding computational requirements. However, current end-to-end deep learning approaches generally fail to predict resonances with high quality-factors (Q-factor). Here, we introduce a universal deep learning strategy that can predict ultra-high Q-factor resonances by decomposing spectra with an adaptive data acquisition (ADA) method while incorporating resonance information. We exploit bound states in the continuum (BICs) with an infinite Q-factor to testify this resonance-informed deep learning (RIDL) strategy. The trained RIDL strategy achieves high-accuracy prediction of reflection spectra and photonic band structures while using a considerably small training dataset. We further develop an inverse design algorithm based on the RIDL strategy for a symmetry-protected BIC on a suspended silicon nitride photonic crystal (PhC) slab. The predicted and measured angle-resolved band structures show minimum differences. We expect the RIDL strategy to apply to many other physical phenomena which exhibit Gaussian, Lorentzian, and Fano resonances.