The most common color of prehnite is green, while yellow prehnite is rare and precious. Heat treatment is usually an effective way to improve the color of gemstones, but whether heat treatment can improve the color of prehnite remains to be explored. In this paper, yellow-green prehnite samples were heat-treated under oxidizing and reducing atmospheres, and the composition, structure and chromogenic mechanism of the prehnite samples before and after the heat treatment were analyzed and summarized by means of X-ray Fluorescence Spectroscopy (XRF), X-ray diffractomer (XRD), in situ high temperature XRD, Fourier Transform Infrared Spectroscopy (FTIR), Micro-Raman Spectroscopy, UV-Vis Spectroscopy, and X-ray photoelectron spectroscopy (XPS). The results show that the change of the relative content and occupation position of Fe²⁺ and Fe³⁺ is the main reason for the color change of yellow-green prehnite. When the yellow-green prehnite is heated to 800 °C, in an oxidizing atmosphere, some of the Fe²⁺ is oxidized to Fe³⁺, the content of Fe³⁺ increases, and the color becomes brownish yellow; in a reducing atmosphere, some of the Fe³⁺ is reduced to Fe²⁺, the content of Fe²⁺ increases, and the color becomes grayish white. The UV-Vis absorption spectra of the oxidized and reduced samples at this temperature further showed that the absorption broadband at 520–700 nm caused by the charge transfer between Fe²⁺ and Fe³⁺ disappeared, resulting in a great change in the color of the prehnite. Our experimental model provides ideas and experimental data for the further study of prehnite heat treatment.