Anthocyanin and lignin content are important indicators of Toona sinensis buds quality. In this study, the appearance morphological and histocytological observations of red and green T. sinensis buds were conducted during storage at 4 ℃ in the dark, and the anthocyanin and lignin content and their related synthetic genes expression levels of in leaf and petiole tissues were analyzed, aiming to provide a theoretical basis for the quality control of T. sinensis buds and the formulation of post-harvest storage and preservation measures. The results showed that: (1) the color of red T. sinensis buds was better after 3 d of storage under low temperature and dark conditions, while black spots began to appear on green T. sinensis buds after 1 d of storage, and the number of black spots gradually increased with the extension of storage time; (2) the leaf veins and petioles xylem cells of red T. sinensis buds were smaller and had fewer cells than that of the corresponding green T. sinensis buds; the secondary cell walls of both red and green T. sinensis buds gradually thickened during storage, and the green T. sinensis buds veins and petiole xylem cells stained more deeply; the xylem cells of red T. sinensis leaf veins and petioles gradually increased in size during storage, while the xylem cells of green T. sinensis bud leaf veins and petioles first increased and then became smaller in size; (3) the anthocyanin content of both red and green T. sinensis buds decreased and the lignin content increased during low temperature storage, and the anthocyanin content of red T. sinensis buds was always higher than that of green T. sinensis buds, while its lignin content was always lower than that of green T. sinensis buds, and the rise and fall of red T. sinensis buds was smaller; (4) the expression levels of anthocyanin and lignin synthesis genes in the leaves and petioles of T. sinensis buds were consistent with the trends of anthocyanin and lignin contents during postharvest low temperature storage, and the expression levels of T. sinensis buds phenylalanine aminolytic enzyme gene (TsPAL) and cinnamic acid-4-hydroxylase gene (TsC4H) showed a trend of first increasing and then decreasing, and the overall trend of decreasing. It was found that both red and green T. sinensis buds underwent lignification and transpiration water loss during storage, and the anthocyanin content decreased and lignin content increased, but green T. sinensis buds had more lignification and severe water loss, and the rise and fall of anthocyanin content and lignin content was greater; the differences in anthocyanin and lignin content of T. sinensis buds were correlated with the expression levels of their synthesis genes. The combined color, appearance, anthocyanin and lignin contents of T. sinensis buds showed that red T. sinensis buds stored longer and were easier to store and preserve than green T. sinensis buds.