X-ray free-electron lasers (XFELs) deliver ultrashort coherent laser pulses in the X-ray spectral regime, enabling novel investigations into the structure of individual nanoscale samples. In this work, we demonstrate how single-shot small-angle X-ray scattering (SAXS) measurements combined with fluorescence and ion time-of-flight (TOF) spectroscopy can be used to obtain size- and structure-selective evaluation of the light-matter interaction processes on the nanoscale. We recorded the SAXS images of single xenon clusters using XFEL pulses provided by the SPring-8 Angstrom compact free-electron laser (SACLA). The XFEL fluences and the radii of the clusters at the reaction point were evaluated and the ion TOF spectra and fluorescence spectra were sorted accordingly. We found that the XFEL fluence and cluster size extracted from the diffraction patterns showed a clear correlation with the fluorescence and ion TOF spectra. Our results demonstrate the effectiveness of the multispectroscopic approach for exploring laser–matter interaction in the X-ray regime without the influence of the size distribution of samples and the fluence distribution of the incident XFEL pulses.