Many mutants of plant induced by heavy ion beam irradiation have been reported in recent years, but leaf anthocyan mutants induced by ion irradiation in evergreen were rarely found. In this study, a color-leaf mutant with purple leaves, stems and petals was isolated from clones of Wandering Jew irradiated by 95.8 MeV/u carbon ion beam. The concentration and histological distribution of leaf pigment were surveyed in wild type and mutant. In mutant, contents of total chlorophylls (Chl), chlorophyll a (Chl a), chlorophyll b (Chl b) and carotenoids (Car) decreased significantly, while concentration of the anthocyanins was 6.2-fold higher than that of wild type. Further composition analysis of anthocyanins by electrospray ionization mass spectrometry (ESI-MS) indicated that the purple pigmentation of leaves in mutant was caused by accumulation of petunidin anthocyanin. Microscopic examination showed that most petunidin anthocyanin accumulated in the lower epidermis, and little in vascular parenchyma of mutant, while there was no pigment in wild type. Meanwhile, in spongy parenchyma of mutant we observed little Chl, which the wild type abounds in. In conclusion, the color-leaf mutant of Wandering Jew induced by irradiation of carbon ions was improved in ornamental value, and it could be contribute to variation in level, component and distribution of foliar pigment. The possible mutation mechanisms were discussed.