As one of the most devastating diseases in Eriocheir sinensis, tremor disease (TD) is caused by Spiroplasma eriocheiris and dramatically increases the economic losses of crab aquaculture. With the development of biotechnology, metabolomics plays an important role in the screening of metabolites related to physiological and pathological changes. In this study, the different metabolites induced by S. eriocheiris were investigated in hemocytes of crab E. sinensis using metabolomics based on GC/MS among diverse phenotypes groups (tremor group, no-symptom group, and control group). Compared with the tremor group, 42 differential metabolites (26 up-regulated and 16 down-regulated) were significantly different in the no-symptom group. The KEGG pathway enrichment analysis showed that the differential metabolites were enriched in “ABC transporters”, “Vitamin B6 metabolism”, “Ascorbate and aldarate metabolism” and “Starch and sucrose metabolism”. The cellobiose and α-ketoglutarate (AKG) were chosen to verify the function of these two metabolites. The crabs were fed with dietary cellobiose (1, 5, and 10 mg/g diet weight) or AKG (1, 5, and 10 mg/g diet weight) before S. eriocheiris injection. The results show that all three concentrations of cellobiose and AKG could reduce the mortality of crabs and decrease the copies of S. eriocheiris in the hemocytes. The histopathological sections of the hindgut of E. sinensis show that cellobiose and AKG affect the connective tissue of the outer layer of muscle. Overall, these results provide insight into TD control and the sustainable development of aquaculture.