Abstract Misfolding and dissociation of Cu, Zn-superoxide dismutase (SOD1) is closely related to the pathogenesis of Amyotrophic Lateral Sclerosis (ALS), so that, it is important to discover the compounds which can stabilize the structure of SOD1 for the prevention and treatment of ALS disease. Caffeoylquinic acids (CQAs), as potential antioxidants, are important bioactive components in multiple vegetables and fruits. In this research, we studied the interactions between the CQAs and SOD1, and explored their effects on stabilizing the SOD1 structure and inhibiting the misfolding of SOD1. Because metal-free SOD1 (apo-SOD1) may be one of the precursor compounds of SOD1 dissociation and aggregation, we investigated the non-covalent complex between CQAs and apo-SOD1 by the electrospray ionization mass spectrometry (ESI-MS) and tandem mass spectrometry (MS/MS). Among the CQAs observed in this research, dicaffeoylquinic acids (di-CQAs) have the stronger binding affinity to apo-SOD1 than monocaffeoylquinic acids (mo-CQAs). In order to study the interactions of di-CQA isomers with apo-SOD1, a novel method based on alkali metal assisted cationization-ion mobility mass spectrometry was established and used to investigate the binding affinity between the di-CQA isomers and apo-SOD1 by distinguishing and quantifying the unbound di-CQA. Collision induced unfolding (CIU), as a new methodology, was further used to assess the stabilities of di-CQAs and apo-SOD1 complexes. The results show that there were no distinct differences in the binding affinity between different di-CQA isomers and apo-SOD1. Furthermore, CIU data obtained in this work reveal that di-CQAs can stabilize apo-SOD1 dimer and retard the unfolding of apo-SOD1 dimer. The strategy developed by us can be also used to study the interactions between other isomeric compounds and target protein in order to discover more potential drug-like small molecules.