Discriminative internal imaging for different chip layers can pinpoint the location of critical defect in the flip chips, yet existing methods face challenges in in-line imaging to identify defects or structures from the sub-surface within the silicon substrate and their underlying coating. To address these challenges, we develop and verify layered elasto-optic models for photoacoustic remote sensing microscopy (PARS) that distinguish structures from multi-layers within a single device for in-line flip-chip wafer inspection. A finite-difference time-domain algorithm based on transparent source (TS-FDTD) accurately predicts different initial slopes of PARS signals within the silicon-metal and the silicon-air models. The initial slopes of PARS signals are experimentally validated and utilized for discriminative non-destructive imaging of the interdigital electrode chips and silicon cracks within the same region of interest. PARS with layered elasto-optic models and non-contact fast scanning has the potential for in-line detection of defects from various layered structures with different refractive indices, offering an approach for discriminative non-destructive testing (NDT) of flip-chip and layered structures.