Yellow silicified scleractinia has gained popularity in the market due to its unique pattern and beautiful color. To comprehend the structural characteristics and color origin of silicified scleractinia, three natural yellow silicified scleractinia were studied using X-ray powder diffractometry, polarising microscopy, thermal field emission scanning electron microscopy, UV-visible spectrophotometry, and Raman spectroscopy. There are differences in the morphology, species, and distribution of quartz particles in the space and the septa area of the scleractinia samples. The quartz particles will develop along the inner wall to the center, with irregular fine grain, xenomorphic medium grain, and xenomorphic semidiomorphic coarse grain when the space between the septa and the theca or the coenosteum is sufficiently large. The quartz particles are mainly xenomorphic or fibrous fine quartz when the cavity is compressed. In the septa area, the quartz particles are mainly fine quartz. The yellow and brownish-red minerals in silicified scleractinia observed under a polarizing microscope were confirmed to be goethite and hematite, respectively. Hematite is the main cause of the yellow color in silicified scleractinia. Due to the influence of coral bone structure, goethite and hematite always exist in the space of very fine or fine quartz particles in the microcosmic form of pigment points. They are enriched in the septa area and the margin of space.