In order to improve the performance and prolong the life of shape memory alloy material (SMA), it is very important to trace and study the microstructure change on the fatigue of SMA. The microstructure features between the samples before and after thermal fatigue (about 100,000 thermal cycles) of the NiTi-SMA films were examined and compared with each other by transmission electron microscopy (TEM) and energy dispersive spectroscopy (EDS). It was found that there is no difference of microstructures between the two kinds of samples except some precipitates appeared in the fatigue specimen. These precipitates which may be identified as TiNi3 phase with a grain size of 10-20 nm may impede transformation from martensite to austenite which works as mechanism of SMA during thermal fatigue. Therefore, these precipitates result in the serious decay on SMA performance and further fracture of the SMA material.