Global climate changes e.g. ocean acidification and warming caused by anthropogenic emission of CO2 are the greatest global threat to coral reef ecosystems. However, compared with the knowledge of Symbiodinium, little is known about the synergistic effects of combined ocean acidification and warming on the coral host and coral-Symbiodinium symbioses. In this study, metatranscriptomic analysis was performed to reveal the response of coral host and its symbiotic Symbiodinium to acidification (A), warming (H) and combined acidification and acidification (AH), using branching A. valida and massive G. fascicularis as models in a laboratory simulation system. RNA-Seq-based differently expressed genes (DEGs), together with coral’s morphological change, suggested the synergistic effects of AH on the coral host and coral-Symbiodinium symbioses, e.g. photosynthesis inhibition and negative effect on nutrients exchange between the host and its Symbiodinium. Particularly, AH showed a far greater impact on coral host than on Symbiodinium. These findings provide novel insights into the molecular mechanism of coral holobionts’ response to future extreme ocean acidification and warming, meanwhile highlight the molecular evidence for the different tolerance of branching and massive corals to environmental changes.