Infection by Hepatospora eriocheir would cause serious disease, hepatopancreatic necrosis disease (HPND), and lead to significant economic losses in Eriocheir sinensis. In this study, the response of E. sinensis during H. eriocheir infection was explored by PCR detection, physiological determination (Masson staining and Calcofluor White staining), electron microscopy, and integrated proteome and metabolome analyses. Pathological and electron microscopy analysis demonstrated that H. eriocheir infection could severely damage the E. sinensis hepatopancreas tissue collagen fibers, muscle fibers, and the cells ultrastructure. Base on the PCR detection and Calcofluor White staining results selected the H. eriocheir positive or negative E. sinensis hepatopancreas used to proteome and metabolome analyses. Using a 2-fold change as a physiologically significant benchmark, total of 370 significantly changed proteins (225 up-regulated proteins and 145 down-regulated proteins) and 386 significantly different metabolites (217 metabolites up-regulated and 169 metabolites down-regulated) in crab hepatopancreas during H. eriocheir infection were identified by proteomic and metabolomic analysis, respectively. Biological analysis of these significantly changed proteins and metabolites showed that the lipid metabolism (for example, glycerophospholipid metabolism, carnitine metabolism, lysolecithin metabolism, biosynthesis of unsaturated fatty acids, sphingolipid metabolism, and linoleic acid metabolism) and energy metabolism (such as tricarboxylic acid cycle (TCA cycle), oxidative phosphorylation, and ATP-binding cassette transporter (ABC transporters)) of E. sinensis hepatopancreas were disproportionally affected by H. eriocheir infection. Meanwhile, several key immune-related processes, proteins or metabolites were activated to against the H. eriocheir infection, for example apoptosis, phagocytosis, oxidative stress, C-type lection, β-1, 3-glucan binding protein, vitellogenin receptor, arginine, leucine, aspartic acid, lysine. This study could provide an insightful view into the response mechanism in E. sinensis hepatopancreas during H. eriocheir infection.