TiNi thin films have attracted wide attentions as actuator materials in the micro-electro-mechanical systems (MEMs) for aerospace craft. However, multiple irradiation, such as the proton, was generally considered as an essential expired factor for the materials used in the aerospace. The present paper focused on the microstructure, martensitic transformation and shape recovery property of TiNi thin films after being irradiated by proton. A single layer structure B19′ phase to a dual-phase (B2 and B19′) with multilayer structure after proton irradiation have been revealed through a combination technique of grazing incidence (GI) XRD and TEM. As-formed irradiated films with amorphous layer and B2 austenite phase displayed a two-step martensitic transformation behavior, which occurred in the irradiated and the unirradiated layer. In contrast, the unirradiated counterparts just exhibited a single-step martensitic transformation. In addition, some defects could be seen after the TiNi films being irradiated. Such defects could induce a stress field that produces the R phase in the B2 phase. Furthermore, the synergistic effect of preferential sputtering effect and inverse Kirkendall effect induced the GP zones in the irradiated layer after 120 keV proton irradiation. The existence of amorphous phase and precipitation significantly deteriorated the shape recovery property.