Investigation of the neutralizing behavior of concrete is essential, as it can help reveal the durability properties of concrete structures. In this paper, anthocyanin extracted from February orchid (F. orchid) petals was used to characterize the neutralized (carbonated, leached, and sulfate-attacked) regions of cement-based materials. The durability of F. orchid indicator was evaluated through comparison between discoloring behaviors of fresh and aged F. orchid indicators, and the capability of the new indicator in neutralization characterization was then verified by combining indicator (phenolphthalein, malachite green, indigo carmine, or thymolphthalein) spray, X-ray computed tomography (CT), and the X-ray attenuation method (XRAM). The result in the present study showed that, with a lower color intensity as compared to phenolphthalein/thymolphthalein, F. orchid indicator was less preferable in studying carbonation but a better choice in characterizing leaching and sulfate attack of cement-based materials. In addition, a sharp carbonation front was revealed in the present study, suggesting that the carbonation process in this study was controlled mainly by diffusion. For leaching and sulfate attack, the broader fronts revealed suggested that both processes were co-controlled by diffusion and reaction. The current work serves as a 'leap' toward the application of natural pigments in analyzing the durability of concrete structures.