Thermostability of proteins in general and especially thermophilic proteins has been subject of a wide variety of studies based on theoretical and experimental investigation. Thermostability seems to be a property obtained through many minor structural modifications. In order to gain better understanding of the thermostability mechanisms of proteins, molecular dynamics simulations of the thermal unfolding reaction of Cyclodextrin glycosyltransferase (EC 2.4.1.19, CGTase) from Bacillus macerans has been carried out for 1.5 ns each at five different temperatures. Distortion of the enzyme is initiated simultaneously in the N- terminal and domain D, while the thermal unfolding of the outer domains of CGTase is faster than that of the catalytic core domain. The catalytic center was well protected by the (a/b)8 TIM-barrel at simulation temperatures up to 600 K. In addition, the unfolding of the 8 b-sheets obeyed the random ordered mechanism, in which the b-sheets 8, 1 and 6 unfolded more rapidly than the others. At the same time, the influences of non-bonded interactions, such as hydrogen bonds and salt bridges, to protein stabilities were also analyzed in detail. The results show clearly that the stability of the protein is not evenly distributed over the whole structure. Our study provides insight into the structure-stability relationship of CGTase, which may help to enlighten our knowledge of protein structural properties, non-bonded interactions that stabilize secondary peptide structures or promote folding and also to better understand their action.