La0.9Sr0.1MnO3 films on Si （100） substrate of different thickness were prepared by sol-gel routine, and the microstructure of LSMO/Si was studied by XRD and confocal micro Raman spectroscopy. Both XRD and Raman results show different structures in LSMO films of different thickness. There are two strong peaks around 490 cm-1and 600 cm-1 that is characteristic of Jahn-Teller distortion in spectra and characteristic peak of rhombohedral structure of the film with thickness of 90 nm, which show the coexistence of two phases. Lattice constants of LSMO film vary with film thickness. Lattice constants vary as film thickness increases, which is because the tilting angle of MnO6 octahedron and the bond length of Mn-O increase as film thickness increases. Raman spectra of 532 nm-laser and 325 nm-laser show, that there are two phases existing in LSMO/Si film, namely the phase in LSMO/Si interface, and the rhombohedral phase in the surface.