A new type of amorphous Fe96Nb4 core soft-magnetic thin film suitable for silicon-based micro-fluxgate was prepared by magnetron sputtering technique. Its phase composition, surface morphology and magnetic hysteresis loop were characterized by X-ray diffractometer, SEM and VSM (vibration sample magnetometer), respectively. The core film was examined by a double-cores fluxgate sensor. The results show that the defects of films decrease when they are prepared at high temperature. Meanwhile, its soft magnetic properties are improved significantly. Silicon-based Fe96Nb4 core thin film prepared at 630 K of the substrate is suitable for the application in the micro-fluxgate iron core materials.