Due to the wide application of plastic products in human life, microplastic pollution in water has recently attracted more attention. Many studies have revealed the size-dependent toxicity of microplastics. Here, we investigated the toxicological effects of polystyrene microplastics (PS-MPs) on the white leg shrimp, Litopenaeus vannamei, a profitable aquaculture species, using a comprehensive histomorphological, microbiome, and metabolomic approach to verify whether smaller particles are more toxic than larger particles. L. vannamei were experimentally exposed to water containing PS-MPs of four sizes (0.1, 1.0, 5.0, and 20.0 μm) for 24 h at 10 mg/L (acute experiment) and 12 d at 1 mg/L (subchronic experiment). After 24 h of acute exposure, PS-MP accumulation in shrimp indicated that the ingestion and egestion of PS-MPs had a size-dependent effect, and smaller particles were more bioavailable. The tissue morphological results of subchronic experiments showed that, for the guts and gills, the smaller sizes of the PS-MPs exhibited greater damage. In addition, 16 S rRNA gene amplicon sequencing showed that the alpha diversity was higher under larger PS-MP exposure. Correlated with changes in intestinal bacteria, we found a greater enrichment of metabolic pathways in hemolymph proteins and metabolites in larger PS-MP groups, such as “arginine and proline metabolism”, “protein digestion and absorption”, “lysine degradation”. Interestingly, the activity or content of biomarkers of oxidative stress showed a peak at 1 μm and 5 μm. Under specific sizes of PS-MPs, the abundance of the pathogen Vibrio and probiotic bacteria Rhodobacter (5-μm) and Bacillus and Halomonas (1-μm) were simultaneously enriched. Our results indicated that PS-MP exposure can cause size-dependent damage to shrimp, yet specific particle size can be influential differently in regard to some research indicators. Therefore, it can enhance our comprehensive understanding of the impacts of microplastics on shrimp health and suggests that specific particle size should be considered when assessing the size-dependent toxicity of microplastics.