In order to explore the key resistance molecules of grass carp, the study was conducted to compare the serum protein expression profiles of the candidate resistant grass carps and the control grass carps using 4D label-free quantitative proteomics. A total of 858 proteins were identified in the grass carp serum, and 329 proteins were differentially expressed in the candidate resistant grass carps and the control grass carps, with 163 up-regulated and 166 down-regulated in the former. The differentially expressed proteins were mainly related to humoral immune response regulation, including complement coagulation cascade, cell adhesion, iron death and other immune-related signaling pathways. Analysis of differentially expressed immune-related proteins showed that the expression levels of humoral immune molecules such as MASP2, C4a, C4b, C7b, C8b, C8g, C9, CFI, C3a.1, C3a.2, C3a.3 and C3a.6 and antigen presentation related immune molecules including MHC1UBA and IGL4V8, were significantly higher in the serum of candidate resistant grass carps than that in the control grass carps, however, the T cell immunity-related molecules, such as TRAV, IGHV1-1, IGHV2-1, IGHV6-1, IGHV3-2 and IGHV11-2, showed lower expression levels in the serum of candidate resistant grass carps. Notably, Western Blot analysis confirmed that humoral immune molecules, represented by C3 and IgM, were highly expressed in the serum of candidate resistant grass carps, which may be associated with the disease resistance of grass carp. The results may provide theoretical basis and molecular reference for the study of disease-related molecules of grass carp and provide molecular resources for the selective breeding of disease-resistant grass carp.