Cobalt (Co) is an important component of vitamin B12, but is toxic to aquatic animals at a high level. In this study, the Pacific white shrimp, Litopenaeus vannamei were exposed to three Co concentrations (0, 100, and 1000 μg/L) for 4 weeks. The survival and condition factor in shrimp exposed to the Co treatments were not different from the control, but the shrimp exposed to 100 μg Co/L gained more weight than in other two groups, and the shrimp exposed to 1000 μg Co/L gained less weight than in other groups. The SOD and GSH-PX activities were higher in shrimp exposed to 100 μg Co/L, but lower in the shrimp exposed to 100 μg Co/L compared with the control, respectively. The MDA contents in the hepatopancreas decreased in the 100 μg Co/L, but increased in the 1000 μg Co/L. The serum lysozyme decreased with ambient cobalt, was lower in the shrimp exposed to 1000 μg Co/L than in other two groups. The expression of C-type lectin 3 was down-regulated by Co concentrations. The Toll and immune deficiency in shrimp exposed to 100 μg Co/L was higher than in other two groups. The mucin-1 was lower in the 1000 μg Co/L group than in other two groups, but mucin-2 and mucin-5AC were higher in the 1000 μg Co/L group than in the control. With increasing Co concentration, Shannon and Simpson indexes of the intestinal microbial communities were decreased. The abundance of pathogenic bacteria (Ruegeria and Vibrio) increased in both Co groups. This study indicates that chronic exposure to waterborne cobalt could affect growth, cause oxidative stress, stimulate the immune response, damage intestinal histology, and reshape intestinal microbiota community L. vannamei.