$La_{0.6}Sr_{0.4}MnO_3$ (LSMO) thin films, which are known as colossal magnetoresistance materials, were prepared on fused silica thin films by conventional RF magnetron sputtering, and the interfacial reactions between them were investigated by rapid thermal processing. Various analyses, namely, X-ray diffraction, transmission electron microscopy combined with energy adispersive X-ray spectrometry, and secondary ion mass spectrometry, were performed to explain the mechanism of the interfacial reactions. In the case of an LSMO film annealed at $800^{circ}C$, the layer distinction against the underplayed $SiO_2$ was well preserved. However, when the annealing temperature was raised to $900^{circ}C$, interdiffusion and interreaction occurred. Most of the $SiO_2$ and part of the LSMO became amorphous silicate that incorporated La, Sr, and Mn and contained a lot of bubbles. When the annealing temperature was raised to $950^{circ}C$, the whole stack became an amorphous silicate layer with expanded bubbles. The thermal instability of LSMO on fused silica should be an important consideration when LSMO is integrated into Si-based solid-state devices.