Typhoid fever is one of many illnesses caused by Salmonella typhi (S. typhi), especially multidrug-resistant (MDR) S. typhi. This research aimed to isolate and quantify MDR S. typhi by detecting specificgenes responsible for MDR S. typhi and the use of Achillea millefolium leaves(A. millefolium L.) essential oil, extract, and nanoparticles separately as all-natural remedies for MDR S. typhi strains. S. typhi was discoveredin 52/84 (61.90%) of the collected specimens from Abbassia Fever Hospital, Egypt. 24/52 samples were multidrug-resistant. However, men were likely more susceptible to infection than women. The findings showed that 91.66% of S. typhi isolates harboured the blaCMY-2 gene, 87.50% harboured the DHFR gene and 50.0% harboured the acrB gene, while 33.33% of them carried the three genes. Gas chromatography-mass spectrometry (GC–MS) exhibited that the cyclohexane,1-methylene-4-(1-methylethyl) compound was the most popular component, with a percentage of 44.5% in A. millefolium L. essential oil. 30µg/ml of A. millefolium L. nanoparticles was found to be the minimal bactericidal concentration (MBC) and the minimal inhibitory concentration (MIC) was 20µg/ml. Consequently, as detected by transmission electron microscopy (TEM), A. millefolium L. nanoparticles damaged the cell wall and cytoplasmic structures of MDR S. typhi. The IC50 of A. millefolium L. nanoparticles against human gastric epithelial cell line (GES1) was 552.023±32.7ug/ml, and the meropenem drug was 151.386±8.32ug/ml, showing that meropenem was more cytotoxic on GES1 normal cells than A. millefolium L. nanoparticles. A. millefolium L. nanoparticles have high effect against MDR S. typhi and more safe than using meropenem drug.