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Apple (Malus domestica, L. Borkh.) is an economically important fruit tree in the world and the quality of apple is vital for better economic returns. Components that determine apple fruit quality may accumulate at different developmental stages. To elucidate molecular mechanisms of compositional change, we performed a comprehensive transcriptomic analysis of apple fruit at five developmental stages, from young fruit to maturity, coupled with metabolic profiling. Correlating the transcriptomic and metabolic processes in apple is important for the understanding of apple fruit quality. We identified 7404 differentially expressed genes (DEGs) and divided them into 9 clusters. This transcriptomic dataset presents a global view of the critical pathways involved in apple fruit development and metabolism at different developmental stages. Physiological quality indices, including firmness, soluble solids content, total titratable acid, sugar content, and acid content, were also characterized during five periods of the apple. The main KEGG pathways, such as starch and sucrose metabolism, glycolysis/gluconeogen metabolism, and the tricarboxylic acid cycle, were analyzed. The activity of enzymes corresponding to DEGs, including sucrose synthetase, sucrose-phosphate synthase, and malate dehydrogenase, involved in the starch and sucrose metabolism and tricarboxylic acid cycle, were analyzed. Moreover, our findings imply that the probable reason of increases in sugar content during apple fruit development is related to a synthesis of trehalose-6-phosphate and trehalose, which are mainly regulated by Trehalose-6-phosphate synthase, trehalose-6-phosphate phosphatase, and trehalase. These analyses using the transcriptomic approach lay the foundation for understanding of apple fruit sugar and acid accumulation during growth and development.