Water is a clean, safe, environmentally benign chemical reaction medium. Understanding the properties of water and the chemical processes in hydrothermal systems is of vital significance in the research of condensed matter chemistry. The physicochemical features of water under hydrothermal conditions greatly differ from that under normal condition, and thus the hydrothermal technique has been extended to much broader systems. In this review article, we introduce the structures of water and its clusters, the variation of their properties along with conditions, and relevant condensed matters in hydrothermal systems. We also illustrate the hydrothermal chemistry through discussing the preparation of typical materials through hydrothermal methods, hydrothermal organic reactions, and bio-hydrothermal chemistry. By relating condensed matter and hydrothermal chemistry, we hope this review will offer new ideas for comprehending hydrothermal reaction systems from the angle of condensed matter chemistry.