Water quality analysis and virus detection was carried out in a shrimp breeding cooperative in Fengxian District, Shanghai in order to understand the correlation between water quality and diseases occurrence of Litopenaeus vannamei. Combined with situation of disease occurrence, principal component analysis (PCA) and orthogonal projections to latent structures discrimination analysis (OPLS-DA) were used to figure out the difference of water quality with in same period among healthy group, virus carrying group and diseased group, and find those water quality factors that contributed most to the differences among three kinds of groups.In this research, shrimp hemocyte iridescent virus was detected in some shrimp samples and the results showed that: (1) Obvious water quality difference existed between diseased group and healthy group, also between diseased group and virus carrying group. While no obvious difference was found between healthy group and virus carrying group without disease out breaking. (2)The correlation degreefrom high to low between water quality factors and the occurrence of shrimp disease is total nitrogen > water temperature > total phosphorus > dissolved oxygen.(3) Mechanical operations such as diversion might cause stress response of shrimp and then induce disease. (4) Shrimp of “virus carrying & healthy group” was cultured in green house and water temperature was kept around 30 ℃, even if shrimp hemocyte iridescent virus was found, cultured shrimpcould grow normally; But when shrimp was transferred to lower temperature ponds, disease broke out.So water quality including temperature, etc., should be paid attention during the breeding of Litopenaeus vannamei and unnecessary mechanical operation activities should be avoided.