Collagen has a unique triple helix structure, which is quite different from that of other proteins and a basis of its special effects. However, collagen triple helix structure is sensitive to environment and easy to be damaged. Recently, microwave has been used more frequently in collagen extraction and modification processes, however, there is few research of microwave irradiation on collagen structure. In this study, collagen was extracted from cattle tendon at first; then 05 mg·mL-1 collagen solution was irradiated with microwave at 30 ℃ as an experiment sample, at the same time, collagen with water bath heating and without heating as controls; finally, the Ultraviolet-Visible Spectroscopy, and Flourier Transformation Infrared Spectroscopy, Circular Dichroism and Fluorescent Spectroscopy were used to characterize the changes of collagen triple helix and supermolecular structure under microwave. It was an innovative study of the influence of microwave irradiation on collagen structure. The result showed that water bath heating and microwave could neither destroy the triple helix structure nor make collagen denaturing below the denaturizing temperature. However, microwave had a negative effect on collagen aggregation compared with water heating. In the interaction between microwave irradiation and collagen, there are both thermal effect same as traditional heating and non-thermal effect representing as negative effect on collagen aggregation. This research would provide a scientific basis of collagen structures and properties under microwave irradiation.