Ionomics is a new multidisciplinary scientific field for investigating the composition and distribution of all chemical elements in specific biological systems as well as their variations under different physiological and pathological conditions. It combines both high-throughput techniques for element profile measurement and bioinformatic methods, which provides new ideas for obtaining a systems-level understanding of biological utilization and functions of these elements. More and more results of researches suggest that ionomics has important theoretical and practical values in etiological study, early diagnosis and screening, and therapeutic strategy selection for complex diseases. In this review, we focus on current advances in the ionomic studies of several complex diseases, which may help further understand the effect and important properties of individual elements, as well as their dynamic ionomic networks in the occurrence and development of diseases.