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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 <inline-formula> <math display="inline"> <semantics> <msubsup> <mi mathvariant="normal">E</mi> <mrow> <mn>2</mn> <mi mathvariant="normal">g</mi> </mrow> <mn>1</mn> </msubsup> </semantics> </math> </inline-formula> 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&#8722;substrate interaction, and are of great significance to researches on bilayer-stacked structures including twisted bilayer structure, Van der Waals hetero- and homo-structure.