Alpinia oxyphylla (Yizhi) is an economically valuable plant, not only used as edible fruit, but also as an important traditional medicinal material. However, there are few studies on fruit development and metabolic pathways. To elucidate the dynamic changes of metabolites and transcription levels during fruit development of A. oxyphylla, the four parts of A. oxyphylla fruit from different periods, including early fruit (EF), middle fruit (MF), late pericarp (LP) and late seed (LS) were collected. KEGG pathway analysis shows that DEGs in EF, MF, LP are involved in amino sugar and nucleotide sugar metabolism, starch and sucrose metabolism, and plant hormone signal transduction. However, at the late part of fruit development (LS), most of the DEGs between LS and LP were enriched in pyruvate metabolism, glycolysis/gluconeogenesis, tryptophan metabolism. We found that in the early and middle parts of fruit development (EF, MF), many differential metabolites were enriched in piperidine tropane and biosynthesis of secondary metabolites, pyridine alkaloid biosynthesis. In addition, important active components, such as nootkatone in A. oxyphylla fruits accumulated in the LS part, but did not show significant differences in the first three parts. Some key transcription factors that are significantly positively correlated with the maturation of AOF have also been identified. Together, our research provides new insights into the accumulation of metabolites and the dynamic changes of the transcriptome during fruit development.