In this study, the functional leaves of color spotted pepper mutant were used as test materials. By observing the microstructure and ultrastructure of different leaf spots, we analyzed the color developing parts, color developing characteristics, number and morphological changes of organelles, and discussed the causes of complex leaf color of color spotted pepper at the cellular level. The results show that: (1) the color of cotyledons mutants were purple, and heterochromatic patches appeared from the first true leaf. There was no obvious regularity in patch location, frequency and color depth. (2) Leukoplakia occured when the chloroplasts in mesophyll cells were reduced or even absent. The uneven distribution of pigment glycosides in mesophyll cells was the main reason for different purple depths, which were distributed both in mesophyll cells and guard cells. (3) The cell morphology and organelle structure in the green spot region of pepper color spot mutant were good; The cells in purple and white spots were moderately swollen, and the organelles were obviously abnormal. (4) The reason for the color of leaves is that there are few or even missing chloroplasts in mesophyll cells and the uneven distribution of anthocyanins. The leaf spot type belongs to pigment type.