Ti-Ni shape memory alloy (SMA) thin films are very attractive material for industrial and medical applications such as micro-actuator, micro-sensors, and stents for blood vessels. An important property besides shape memory effect in the application of SMA thin films is the adhesion between the film and the substrate. When using thin films as micro-actuators or micro-sensors in MEMS, the film must be strongly adhered to the substrate. On the other hand, when using SMA thin films in medical devices such as stents, the deposited alloy thin film must be easily separable from the substrate for efficient processing. In this study, we investigated the effect of substrate roughness on the adhesion of Ti-Ni SMA thin films, as well as the structural properties and phase-transformation behavior of the fabricated films. Ti-Ni SMA thin films were deposited onto etched glass substrates with magnetron sputtering. Radio frequency plasma was used for etching the substrate. The adhesion properties were investigated through progressive scratch test. Structural properties of the films were determined via Feld emission scanning electron microscopy, X-ray diffraction measurements (XRD) and Energy-dispersive X-ray spectroscopy analysis. Phase transformation behaviors were observed with differential scanning calorimetry and low temperature-XRD. Ti-Ni SMA thin film deposited onto rough substrate provides higher adhesive strength than smooth substrate. However the roughness of the substrate has no influence on the growth and crystallization of the Ti-Ni SMA thin films.