Cyclodextrin glycosyltransferase (EC2.4.1.19, CGTase) catalyzes the formation of cyclodextrins from starch. Thermal stability is of great importance for this enzyme. In order to gain better understanding of the thermostability mechanisms of the protein, we herein report structural features of the CGTase B domain at different temperatures. The present study mainly focuses on the contribution of non-covalent intramolecular interaction to protein stability and how they affect the thermal stability of the enzyme. Profile of root mean square fluctuation identifies thermostable and thermosensitive regions of the B domain. Analyses of trajectories in terms of secondary structure content, intramolecular hydrogen bond and salt bridge interactions indicate distinct differences in different temperature simulations. A detailed investigation of this domain suggests that the geometry of this domain is well protected by the critical intramolecular interaction up to 500 K temperature. The results also show clearly that main chain-main chain hydrogen bond and salt bridge are of major importance in protein stability at elevated temperature. Principal component analysis suggests that the motion of the B domain as well as the critical residue is similar at different temperatures. According to above-mentioned observations, the destabilization of region may be compensated by the formation of salt bridge and hydrogen bond that have been used as an evolutionary mechanism by the mesophilic enyme. The present work is an effort to extract more deterministic features of thermal stability from its dynamic nature much during the initial stages of denaturation.