A novel, simple, and rapid method, named cell membrane affinity extraction (CMAE)-offline liquid chromatography timeof-flight mass spectrometry (LC-TOF-MS) was developed for screening and identifying antimicrobial peptides from Jatropha curcas meal protein isolate hydrolysates (JCMPIH) obtained by proteolytic enzyme (pepsin, trypsin, protamex, neutrase, flavourzyme, papain, alcalase, and acid protease) hydrolysis. A cationic antimicrobial peptide (CAILTHKR, JCpep8) was successfully isolated and identified by this method. Antimicrobial assay indicated that JCpep8 was active against the tested microorganisms (Escherichia coli ATCC 25922, Shigella dysenteriae ATCC 51302, Pseudomonas aeruginosa ATCC 27553, Staphylococcus aureus ATCC 25923, Bacillus subtilis ATCC 23631, Streptococcus pneumoniae ATCC 49619) with minimal inhibitory concentration values ranging from 29 to 68 µg/mL. JCpep8 induced significant morphological alterations of the tested microbe surfaces, as shown by transmission electron microscopy, indicating strong membrane disruption. The results showed that CMAE-offline LC-TOF-MS could be a promising method for discovering high-throughput screening antimicrobial peptides from JCMPIH.