Microplastics (MPs) pose a major threat to marine life and ecosystems. However, the toxicological effects of MPs on crustaceans which are highly susceptible to MPs pollution are not fully understood. In addition, MPs can serve as the medium for pathogens, increasing the risk of disease outbreaks in shrimp aquaculture. To study the biological risks of MPs close to the aquacultural practice, the current study firstly focused on the impacts of MPs colonized by the pathogen Vibrio parahaemolyticus on shrimp Litopenaeus vannamei. The role of microplastics in facilitating pathogens infection of shrimps was firstly reported. Under this impact, the hepatopancreas of L. vannamei suffered severe damage. At 96 hpi, the shrimp mortality rate reached 100%. Dominant phyla altered in the intestinal and hepatopancreatic microbiota of L. vannamei. The characterization of the L. vannamei microbiota under the condition where the pathogens and MPs exist in the surroundings, to be used as a reference for comparison with healthy and diseased shrimp in the aquacultural system, is necessary.