Actinidia arguta 'Tianyuanhong' is a new kiwifruit variety with an all-red pericarp and pulp, in contrast to the all-green pulp of A. arguta 'Yongfengyihao'. Transcriptome profile analysis of fruit color has been reported, however, the metabolic mechanisms producing red flesh remain unknown, and it is unclear why the pulp of 'Tianyuanhong' is red rather than green. Herein, we identified differences between the proteomes of two A. arguta cultivars with different fruit color by using iTRAQ-based quantitative proteomic methods during the stage of color change. In total, 2310 differentially abundant proteins were detected between the two cultivars at 70 and 100 days after flowering, and the protein functions were analyzed based on KEGG and GO. The largest group of differentially expressed proteins were related to photosynthesis, glyoxylate metabolism, N metabolism, and anthocyanin biosynthesis. Finally, to verify the iTRAQ data, 12 representative genes encoding differentially expressed proteins were analyzed via quantitative real-time PCR, and these genes differed in transcriptional and translational expression levels. Our proteomic study contributes to understanding the metabolic pathways and biological processes involved in fruit color changes in different cultivars of A. arguta. These data and analyses will provide new insight into the development of kiwifruit flesh color.