Even though microplastics (MPs) and graphene nanomaterials (GNMs) have demonstrated individual toxicity towards aquatic organisms, the knowledge gap lies in the lack of understanding regarding their combined toxicity. The difference between the combined toxicity of MPs and GNMs, in contrast to their individual toxicities, and furthermore, the elucidation of the mechanism of this combined toxicity are scientific questions that remain to be addressed. In this study, we examined the individual and combined toxicity of three polystyrene microplastics (MPs) with different functional groups—unmodified, carboxyl-modified (COOH-), and amino-modified (NH2-) MPs—in combination with reduced graphene oxide (RGO) on the freshwater microalga Scenedesmus obliquus. More importantly, we explored the cellular and molecular mechanisms responsible for the observed toxicity. The results indicated that the growth inhibition toxicity of RGO, either alone or in combination with the three MPs, against S. obliquus increased gradually with higher particle concentrations. The mitigating effect of MPs-NH2 on RGO-induced toxicity was most significant at a higher concentration, surpassing the effect of unmodified MPs. However, the MPs-COOH did not exhibit a substantial impact on the toxicity of RGO. Unmodified MPs and MPs-COOH aggravated the inhibition effects of RGO on the cell membrane integrity and oxidative stress-related biomarkers. Additionally, MPs-COOH exhibited a stronger inhibition effect on RGO-induced biomarkers compared to unmodified MPs. In contrast, the MPs-NH2 alleviated the inhibition effect of RGO on the biomarkers. Furthermore, the presence of differently functionalized MPs did not significantly affect RGO-induced oxidative stress and photosynthesis-related gene expression in S. obliquus, indicating a limited ability to modulate RGO genotoxicity at the molecular level. These findings can offer a more accurate understanding of the combined risks posed by these micro- and nano-materials and assist in designing more effective mitigation strategies.