In this paper, the quality of Phyllanthus emblica was evaluated by establishing a comprehensive taste index and odor component analysis method, and the formation mechanism of quality difference was revealed by mass spectrometry imaging and metabolomics. Studies have found that the representative substances of bitterness and astringency in cultivated PE, such as amlaic acid, kaempferol, quercetin and their derivatives, have higher content. Compared with wild PE, cultivated PE has a very lower 2-Isobutyl-3-methoxypyrazine content, a kind of odor molecule that destroys the fruits flavor. Biological activity studies showed that the biological activity of wild PE was stronger than cultivated PE. Mass spectrometry imaging revealed significant differences in the distribution of multiple components between the two types of PE. Metabonomic studies show that their quality differences may be related to the difference of flavonoids and flavonol biosynthesis in PE.