A glue filling method for a multilayer thin film sensor structure is disclosed herein. Two outer layers of a composite heat-resistant membrane are carved to have desired patterned holes; an inner layer is interposed between two outer layers to form a layered structure. The composite heat-resistant membrane is stuck onto the multilayer thin film sensor structure with the patterned holes aligned to an electric-conduction through-hole of the multilayer thin film sensor structure to form a filling region. A conductive glue is filled into the filling region. Sustained by the inner-layer heat-resistant membrane, the conductive glue protrudes from the patterned hole to cover a portion of the conductive metals on the surface of the multilayer thin film sensor structure. Thereby are simultaneously achieved a water-proof effect, an airtight effect and a fine interface compatibility.