The stratified structured microsphere cavity with high refractive index shell outer its surface was simulated using the finite-difference time-domain method(FDTD). The energy density distributions of whispering-gallery modes(WGM) in the microsphere cavity have been analyzed,and resonance performance of stratified structured microsphere cavities with different shell thickness were compared too. Then the methods to tune the microsphere cavity or to control the resonant modes of microsphere cavity were presented and discussed. With this stratified structure,an effective enhance was achieved for the resonant performance of microsphere cavity(with Q value 30% larger and mode volume 60% smaller than the homogeneous structured microsphere cavity). These studies and results provide new optimizing methods for the subsequent structure design and practical application of microsphere cavity.