‘Kuerlexiangli’ (Pyrus sinkiangensis Yu) is an important market pear in China. The shape and the quality of fruits are negatively affected by the presence of a persistent calyx. To explore the molecular mechanism of calyx abscission, different protein expressions were identified at two critical processes of the calyx abscission under three treatments: an abscising treatment (6000 × Flusilazole + 300 × PBO), a persisting treatment (50 mg/L GA₃) and a water control. The collected protein fragments were investigated to identify candidate proteins and perform relative quantification using isobaric tags for relative and absolute protein quantitation (iTRAQ). In this study, a total of 378,078 spectra and 3873 proteins were identified. Among them, 2371 differentially abundant proteins (DAPs) had Gene Ontology terms and were related to 124 defined pathways from the Kyoto Encyclopedia of Genes and Genomes. Some important DAPs relating to calyx abscission were mainly involved in photosynthesis, plant hormone signal transduction, cell-wall modification, and carbohydrate metabolism. Quantitative real-time polymerase chain reaction was used to confirm the expression patterns of some important genes. Among the isolated candidate proteins, we identified the proteins that exhibited highly dynamic expression changes and polygalacturonase and chitinase appeared to play key roles during the process of calyx abscission. These proteins are important candidate proteins for future functional identification and exploring the mechanism of calyx abscission. This study will enhance our knowledge of the biological basis of fruit sepal shedding, and provide more references for improving the calyx abscission rate and fruit quality of pear fruit.