Background: Yellow Camellia is a kind of rare plant with high economic and medicinal value. It is known as the "giant panda" of the botanical world. Camellia group of plants (Camellia Sect. Chrysantha Chang) is the only golden flower of Theaceae. Compared with Camellia nitidissima, Camellia limonia grows in karst areas, where the soil has the characteristic of high calcium content. However, there are few studies about the Camellia limonia in karst soil environment and the adaptation mechanism is no clear. Results: In this study, we found that under high calcium treatment, the chlorophyll content and leaf areas of Camellia limonia increased, while those of Camellia nitidissima decreased. The photosynthetic efficiency of Camellia limonia was more stable and higher than Camellia nitidissima. Compared with Camellia nitidissima, the conductance was larger and the degree of leaf shrinkage was smaller in Camellia limonia. The metabolomics analysis showed that the kaempferol-3-o-rutinoside, tyrosol, 6-o-methyldeacetylisoipecoside and (r)-mandelic acid are the main differently metabolic compounds . The results of karst high calcium soil metagenomics showed that microbacterium-testaceum, intrasporangium-calvum and rubrivivax-gelatinosus significantly changed. Through metabonomics and metagenomics integrative analysis, flavone and flavonol biosynthesis is suggested to be the main regulation pathway, which is regulated by apigenin, kaempferol, astragalin, isoquercitrin metabolites and TT7, UGT78D1, UGT78D2 genes. This metabolic pathway involves the synthesis of flavonoids. Flavonoids have the functions in drought and salt resistance, which play an important role in the adaptation of Camellia limonia in karst high calcium environment.Conclusion: This omics study identified key regulation metabolites and genes for Camellia and provided important basis for the adaptive mechanism of plants to adapt to the high-calcium environment and the protection of Camellia species.