Fluorinated graphdiyne (F-GDY) materials exhibit exceptional performance in various applications, such as luminescent devices, electron transport, and energy conversion. Although F-GDY has been successfully synthesized, there is a lack of comprehensive identification of fluorinated configurations, either by theory or experiment. In this work, we investigated seven representative F-GDY configurations with low dopant concentrations and simulated their carbon and fluorine 1s X-ray photoelectron spectroscopy (XPS) and carbon 1s near-edge X-ray absorption fine-structure (NEXAFS) spectra. The goal was to establish the structure-spectroscopy relation for these materials. The simulated XPS spectra closely match the experimental data, providing sensitive identifications of certain fluorinated structures, although challenges still persist in distinguishing a few similar configurations. In contrast, the NEXAFS spectra, generated by three non-equivalent carbon atoms at the K-edges, offer more detailed information and are more sensitive for identifying all different F-GDY structures. Our theoretical study provides valuable insights for future experimental identification of F-GDY structures. These findings underscore the utility of computational X-ray spectroscopy in advancing the understanding and development of novel carbon-based materials.