The beryl family is known for its wide range of colors and has always been an important gemstone variety in the market. Over the past few decades, scholars both domestically and abroad have conducted extensive research on the coloration mechanism and color-modification techniques of beryls of different colors. As one of the important coloration transition-metal ions, the valence state regulation of iron ion is critical in the color-modification process of beryls. Therefore, the valence state, site occupancy, and corresponding chromogenic effects of iron ions have always been the focus of beryl research. Iron ions are believed to exist in various sites within the beryl crystal structure, including the aluminum octahedral Al³⁺ site, silicon tetrahedral Si⁴⁺ site, beryllium tetrahedral Be²⁺ site, structural channel 2a or 2b site, and lattice interstitial site 6g, and are the main color-causing elements for blue, green, or yellow beryls. Through a review and comprehensive analysis of the literature on the crystal structure of beryl, site occupancy and the arrangement of outer electrons of iron ions, we suggest that Fe²⁺ and Fe³⁺ play a dominant role in the coloration of blue and yellow beryls, respectively. Further research is needed to determine the specific differences in color-causing effects when Fe²⁺ and Fe³⁺ are located in different sites within the lattice.