Chlorophyll is the primary source of color in widespread green plants. It has been investigated in mung bean seed coats and cotyledons. This study aimed to examine chromatic changes in mung beans during heat processing. It observed pigment variation within the cotyledons and seed coats of mung beans. Following thermal treatment from 0 to 50 min, the color of mung bean products changed, primarily from a decrease in chlorophyll content in the seed coat (from 6.57 to 1.28 mg/100 g, with significant differences. p < 0.05), accompanied by the formation of tawny pheophytin. However, the b value of mung bean seed coat showed an increasing trend with significant differences (yellowness, 21.55 increasing to 34.85, p < 0.05). Interestingly, the total flavonoid content in the seed coat tended to increase with thermal time (2.93 to 18.74 µg/mg) with statistical differences (p < 0.05). The condensation reaction of flavonoids with other polyphenolic compounds formed dark-brown polymers, resulting in a significant decrease in brightness (L value) of the cooking solution with thermal processing time (p < 0.05). Thus, the chlorophyll extraction and purification of the mung bean seed coat confirmed the morphological change of chlorophyll combined with the Maillard reaction, resulting in the color change after thermal treatment. It showed that a significant reason for the discoloration of mung beans was pheophytin from chlorophyll in the processing process.