Increasing atmospheric carbon dioxide results in ocean acidification and warming, significantly impacting marine invertebrate larvae development. We investigated how ocean acidification in combination with warming affected D-veliger larvae of the Pacific oyster Crassostrea gigas. Larvae were reared for 40 h under either control (pH 8.1, 20 °C), acidified (pH 7.9, 20 °C), warm (pH 8.1, 22 °C) or warm acidified (pH 7.9, 20 °C) conditions. Larvae in acidified conditions were significantly smaller than in the control, but warm acidified conditions mitigated negative effects on size, and increased calcification. A proteomic approach employing two-dimensional electrophoresis (2-DE) was used to quantify proteins and relate their abundance to phenotypic traits. In total 12 differentially abundant spots were identified by nano-liquid chromatography-tandem mass spectrometry. These proteins had roles in metabolism, intra- and extra-cellular matrix formations, stress response, and as molecular chaperones. Seven spots responded to reduced pH, four to increased temperature, and six to acidification and warming. Reduced abundance of proteins such as ATP synthase, GAPDH and increase of superoxide dismutase occurred when both pH and temperature changes were imposed, suggesting altered metabolism and enhanced oxidative stress. These results identify key proteins that may be involved in the acclimation of C. gigas larvae to ocean acidification and warming. Significance Increasing atmospheric CO2 raises sea surface temperatures and results in ocean acidification, two climatic variables known to impact marine organisms. Larvae of calcifying species may be particularly at risk to such changing environmental conditions. The Pacific oyster Crassostrea gigas is ecologically and commercially important, and understanding its ability to acclimate to climate change will help to predict how aquaculture of this species is likely to be impacted. Modest, yet realistic changes in pH and/or temperature may be more informative of how populations will respond to contemporary climate change. We showed that concurrent acidification and warming mitigates the negative effects of pH alone on size of larvae, but proteomic analysis reveals altered patterns of metabolism and an increase in oxidative stress suggesting non-additive effects of the interaction between pH and temperature on protein abundance. Thus, even small changes in climate may influence development, with potential consequences later in life.