The pear (Pyrus pyrifolia) is an important accessory fruit in which the pear core is tarter than the pear pulp. However, the reason for the acidic core and diversity in the taste of the same fruit is not clear. In this study, we observed that the citrate contents were three times higher in the core than in the pulp, while the malate content decreased along with fruit development and was significantly lower in the core than in the pulp at 110 days after flowering. Overall transcript levels for citrate-malate synthesis-related genes increased more in the pear core than the pulp at early fruit development, while degradation-related genes activity was nearly similar or non-significant between the core and pulp during fruit development. The lesser malate accumulation in the pear core compared to the pulp at 110 DAF was possibly due to the reduced activity of tDT2 gene. Regarding citrate accumulation, we identified five important p-type H⁺-ATPase genes in pear and found that the relative expression level of the PH8.1 gene was four-fold higher in the core than in the pulp during fruit development. Moreover, the expression level of di-carboxylate carrier gene 2 (DIC2) was constantly and significantly higher in the core than in the pulp. In addition, correlation analysis signified that the transcript levels of the two genes PH8.1 and DIC2 positively and significantly correlated with the citrate contents. These results suggested that the increased and collaborative activity of PH8.1 and DIC2 played a key role in the higher citrate accumulation in the core than the pulp, thus, with the help of molecular breeding tools, the citrate contents can be optimized in pear fruit for divers and improved fruit flavoring.