Plasma-activated water (PAW) indicated promising potential in controlling the biological contamination of Bacillus cereus, which eliminated its evolutionary endospore that improves its survival ability. However, the spore inactivation mechanism by PAW at molecular level was not well understood. The mechanism of the Bacillus cereus endospore against PAW at proteomic levels was demonstrated. The Tandem Mass Tag (TMT) labeling was performed. By comparing the treatment groups with control (including PAW and PAW added superoxide dismutase (SOD)) , the expression of 251 proteins (with the number of 207 up- and 44 down-regulated) and 379 proteins (with the corresponding number of 238 and 141) were drastically affected, separately. The six categories based on the protein-protein interaction (PPI) networks included oxidation-reduction, transport, sporulation and DNA topological change, gene expression, metabolism, and others. The three dehydrogenases (Gene hisD, BC_2176, and asd) in PAW while oxidoreductase (Gene BC_0399 and BC_2529) in SOD were activated to maintain the antioxidation of spores. The proteins (BC_4271 and BC_2655) in SOD were dramatically activated, which were involved in the carbohydrate, amino acid, and energy-coupling transport. All the small, acid-soluble spore proteins were activated in both groups to protect the spores’ DNA. In SOD, genes metG2 and rpmC also were considered important factors in translation while this role was played in gene groES but not rpmF in PAW. The PAW activated the biogenesis of cell wall/membrane/envelope and phosphorelay signal transduction system to contribute to the survival of spores whereas the SOD damaged these two processes as well as cell division, chromosome separation, organic acid phosphorylation, base- and nucleotide-excision repair to lead to the death of spores. This would promise to lay the foundation for advancing the study of the intrinsic mechanism of spore killing against PAW and can also provide a reference for future verification.