The objectives of this work aim to investigate the interaction and cytotoxicity between nanometric graphene oxide (GO) and nasopharyngeal carcinoma cells (NPC-BM1), and possible application in photon therapy. GO nanosheets were obtained in the size range of 100–200 nm, with a negative surface charge. This nanometric GO exhibited a limited (<10%) cytotoxicity effect and no significant dimensional change on NPC-BM1 cells in the tested GO concentration range (0.1–10 µg·mL−1). However, the secondary protein structure was modified in the GO-treated NPC-BM1 cells, as determined through synchrotron radiation-based Fourier transform infrared microspectroscopy (SR-FTIRM) mapping. To further study the cellular response of GO-treated NPC-BM1 cancer cells at low GO concentration (0.1 µg·mL−1), photon radiation was applied with increasing doses, ranging from 2 to 8 Gy. The low radiation energy (<5 Gy) did not cause significant cell mortality (5–7%). Increasing the radiation energy to 6–8 Gy accelerated cell apoptosis rate, especially in the GO-treated NPC-BM1 cells (27%). This necrosis may be due to GO-induced conformational changes in protein and DNA/RNA, resulting in cell vulnerability under photon radiation. The findings of the present work demonstrate the potential biological applicability of nanometric GO in different areas, such as targeted drug delivery, cellular imaging, and radiotherapy, etc.