This work reports the interlayer difference of exciton and phonon performance between the top and bottom layer of a bilayer-stacked two-dimensional materials structure (BSS). Through photoluminescence (PL) and Raman spectroscopy, we find that, compared to that of the bottom layer, the top layer of BSS demonstrates PL redshift, Raman E 2 g 1 mode redshift, and lower PL intensity. Spatial inhomogeneity of PL and Raman are also observed in the BSS. Based on theoretical analysis, these exotic effects can be attributed to substrate-coupling-induced strain and doping. Our findings provide pertinent insight into film-substrate interaction, and are of great significance to researches on bilayer-stacked structures including twisted bilayer structure, Van der Waals hetero- and homo-structure.