This study was conducted to assess the molecular mechanism of meat quality between low- and high-pH muscles using two-dimensional gel electrophoresis (2DE) with matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI–TOF/MS) on longissimus dorsi muscles from Berkshire species, assigned to high- (5.92 ± 0.02) and low-pH groups (5.55 ± 0.03). The high-pH group had a lower lightness, yellowness, drip loss, shear force, and a higher National Pork Producers Council color than the low-pH group. The meat quality changes were related to the altered protein expression between the two groups. Fourteen protein spots were identified by MALDI–TOF/MS and among them, nine proteins involved in meat quality attributes significantly increased: the alpha-crystallin B chain, dual specificity phosphatase 1, vimentin X1 and X2, ATP synthase subunit d, mitochondrial (ATP5H), peroxiredoxin 6 (PRDX6), ubiquitin carboxyl-terminal hydrolase 14 (UCTH14), and cytochrome c. Moreover, the proteins’ translation efficiency was analyzed by their mRNA expression via quantitative polymerase chain reaction. An increase in the mRNA levels of ATP5H, PRDX6, and UCTH14 is consistent with protein expressions. These results may provide valuable information to decipher the molecular mechanism behind meat quality of low- and high-pH muscles.