White feces syndrome (WFS) has been one of the emerging diseases causing instructive economic losses in the penaeid shrimp aquaculture industry, though the etiology of WFS remains unclear. In this research, we have collected intestinal samples from normal and diseased shrimp (Litopenaeus vannamei) from the natural shrimp cultivation farm for histological and proteomic analysis. The preliminary pathogen detection confirmed that WFS in this study was (Enterocytozoon hepatopenaei) EHP-WFS that was related to Vibrio spp. Moreover, the destructive damage of the intestine in WFS-diseased shrimp revealed by histological observation indicated a deficiency in digestive capacity, which might be closely related to WFS. Furthermore, we have characterized 86 and 165 differentially expressed proteins (DEPs) through a non-directional integrative analysis, which were significantly up-regulated and down-regulated, respectively. The down-regulation of various digestive enzymes in the WFS-diseased shrimp was consistent with the results of intestinal histology. DEPs were enriched in the lysosome and sphingolipid metabolism pathway, indicating that they were strongly associated with the occurrence of WFS (P <
0.05). Of this, the expression of down-regulated proteins in the lysosomal pathway was further validated by real-time quantitative polymerase chain reaction (RT-qPCR). Ultimately, crustin, lipase, and glucosylceramidase (GBA), which were significantly decreased in WFS-diseased shrimp, were screened as the predictive protein signatures for the diagnosis and prevention of WFS. Consequently, our results will provide a theoretical reference for the diagnosis of EHP-WFS by the protein aspect and crustin, lipase, and GBA may be predictive signatures that are suitable for EHP-WFS.