Graphene family nanomaterials are used in a broad range of applications. These materials have been released into the aquatic system where they can have toxicological effects in non-target organisms. Although several studies have investigated their toxicity, there is little information on the toxicity and mechanisms of graphene nanomaterial mixtures in Microcystis aeruginosa. This study investigated the toxicities of individual and binary mixtures of graphene family nanomaterials (graphene oxide (GO), GO quantum dots (GOQD), and carboxylic acid-functionalized single-walled carbon nanotubes (C-SWCNT)) in M. aeruginosa. The toxicological interaction profiles of the mixture rays were also examined. The results showed that the three types of nanoparticles and their binary mixture rays had significant inhibitory and hormetic effects in M. aeruginosa. Metabolomics analysis showed that the nanomaterials had different toxicity mechanisms. Amino acid metabolism was sensitive to GO exposure, while C-SWCNT and GOQD exposure led to a sharp decline in sugars and an increase in fatty acids, respectively. The toxicological interactions in the binary GO and GOQD mixtures were different from that of the GO and C-SWCNT mixtures. These findings increase our understanding of the nanotoxicity and toxicity mechanisms of GO, C-SWCNT, and GOQD and will aid in the risk assessment of nanomaterials in aquatic environments. Amino acids, sugars, and