This data article presents a differentially mitochondrial proteomic dataset in human ovarian cancer tissues relative to control tissues. The mitochondrial samples were prepared from human ovarian cancer and control ovary tissues, and were digested with trypsin. The tryptic peptides from ovarian cancer and control mitochondrial samples were labeled by isobaric tags for relative and absolute quantification (iTRAQ) reagents, followed by strong-cation exchange (SCX) chromatography, liquid chromatography (LC)-tandem mass spectrometry (MS/MS), and bioinformatic analysis. This data article is related to a published article (Li et al., 2018) [1].