Separation of antioxidant compounds (caffeoylquinic acids (CQAs), phenolics, melanoidin, and caffeine) from green coffee beans with hydrothermal extraction and decomposition kinetics of 3-o-caffeoylquinic acid (3-CQA) are reported. Antioxidant capacity (AOC) of the extracts increased as extraction temperature was increased up to 410 K and then it decreased up to extraction temperatures of 500 K. As extraction temperature was further increased above 500 K, AOC remarkably increased The decomposition rate of 3-CQA in water was determined from 433 to 513 K. The increase and decrease in AOC with extraction temperature can be attributed to the hydrolysis of oligomeric structures (glycosides) in the coffee beans that yield CQAs, the decomposition of the CQAs, and to the formation of melanoidins that had a characteristic brown color. Hydrothermal extraction provides an effective method for the separation of antioxidant compounds from green coffee beans, and the effluent extracts may be suitable for food products.