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Understanding the relationship between molecular structure at the microscale and spectral behavior is essential for designing functional materials. Here, we report how the chemical structure, π-conjugation, and intermolecular interactions jointly modulate Raman spectroscopy, fluorescence, and excited-state lifetimes of seven molecules. The charge-coupled device (CCD) camera and field-emission scanning electron microscopy (FE-SEM) image the powders of these molecules to reveal the microscale particle crystal morphology. In contrast, a scanning tunneling microscope (STM) images the molecules to reveal their intermolecular interactions (hydrogen bonding, halogen bonding, and ionic interaction) during crystallization. The Stokes and anti-Stokes Raman spectra of 2,6-naphthalenedicarboxylic acid, biphenyl-4,4′-dicarboxylic acid, and dodecanedioic acid powders all exhibit distinct Raman signatures of their carbon skeletons. With increasing the laser excitation power, these Stokes Raman peaks show a linear power relationship, while the anti-Stokes Raman peaks show a second-order polynomial (nonlinear) power dependency. In comparison, 2,2′:6′,2″-terpyridine-4,4′,4′′-tricarboxylic acid does not show any Stokes or anti-Stokes Raman peaks, while 6,6′′-dibromo-2,2′:6′,2′′-terpyridine (DT) shows obvious Stokes Raman peaks. The DT’s Raman peaks show a second-order polynomial (nonlinear) power dependence. Furthermore, sodium acrylate shows a series of Stokes and anti-Stokes Raman peaks, with predominantly linear power dependency. However, sodium propiolate shows much weaker Stokes and anti-Stokes Raman spectra. In general, density functional theory (DFT)-calculated Raman spectra of the seven molecules show good agreement with the experimental Raman spectra. Further, the fluorescence and lifetime spectra of these seven molecules are measured, which could also reflect the properties of their chemical structure, π-conjugation, and intermolecular interactions. Moreover, the attenuated total reflection Fourier transform infrared spectroscopies (ATR-FTIR) of these seven molecules also verify the carboxylic acid or carboxylate fingerprints, agreeing well with Raman spectra. This work provides an integrated Raman, fluorescence, ATR-FTIR, CCD, FE-SEM, and STM study of organic molecules to reveal their chemical structure, π-conjugation, and intermolecular interaction differences.