The influence of natural and anthropogenic impacts on coral reefs were taken into account in order to understand such effects as bleaching, coral diseases and ocean acidification. Recently, more frequent coral bleaching events are strongly impacting reef systems as a consequence of elevated sea-surface temperature （SST） during longer periods. Increased coral mortality is the result of extreme bleaching events and surviving corals are being weakened with decreasing reproductive potential, slower growth and decreased calcification, leaving them vulnerable to infectious diseases. However, recent reports show that coral adapts under the effects of multiple stresses on coral physiology with chemical and biological responses for coral adaptation. This is due to the high complexity of the “coral holobiont”（ coral in symbiosis with its zooxanthellae and a microbial community that maintain a delicate balance to keep coral healthy）. We presented a novel viewpoint of bleaching mechanisms based on studies done at micro/nano size scales: The study revealed that bleaching is not the result of expelling zooxanthellae to the surrounding waters, but rather results from the degradation of damaged zooxanthellae inside coral tissues as a new adaptive strategy by changing from chlorophyl a to cycloenol. Recent studies show that coral will adapt under high temperature based on the response of various chemical signals like glycerol, HSP, fluorescence protein and bacteria. For the future of coral reefs, it is necessary to study the molecular level from micro-nano and molecular scales.