How the particle size and concentration of microplastics impact their toxicity is largely unknown. Herein, the effects of polystyrene microplastics (1 μm, MPs) and nanoplastics (100 nm, NPs) exposed at 1 mg/L (L) and 10 mg/L (H), respectively, on the growth, histopathology, oxidative stress, gut microbiome, and metabolism of rare minnow (Gobiocypris rarus) were investigated by chemical analysis and multi-omics. MPs and NPs inhibited the growth, induced histopathological injury and aggravated oxidative stress markedly with contrasting significance of particle size and concentration. The composition of core gut microbiota changed dramatically especially for the MPs-H. Similarly, gut bacterial communities were reshaped by the MPs and NPs but only NPs-H decreased both richness and Shannon indexes significantly. Co-occurrence network analysis revealed that the potential keystone genera underwent great changes in exposed groups compared to the control. MPs-H increased the network complexity and the frequency of positive interactions which was opposite to other exposed groups. Moreover, the metabolomic profiles associated with amino acid, lipid, unsaturated fatty acid and hormone metabolism were disturbed significantly especially for MPs-H and NPs-H. In conclusion, the toxicity of MPs depends on both the particle size and concentration, and varies with the specific indicators as well.