Nanoparticles (NPs) have received much attention recently in various areas of industry, biomedical, and agricultural sectors worldwide. It is important to recognize the consequences of the use and application of NPs and their interaction with ecosystems components including plants, whether in the environmental area or in physiology and crop production. The present study aimed to investigate the changes in essential oil content and composition of Thymus daenensis Celak., Thymus fedtschenkoi Ronniger and Thymus vulgaris L. under silver nanoparticles (AgNPs) and silicon nanoparticles (SiNPs) in four levels (0, 30, 60, 100 ppm). The essential oil content increased at all stress levels and in all three species. The amount of monoterpene hydrocarbons in T. fedtschenkoi increased, while it decreased in other two species. The amount of sesquiterpentes, except for oxygenated sesquiterpenes in T. daenensis, increased slightly. Compared to other factors, the type of plant species was more determinative in response to treatments. Overall, both AgNPs and SiNps treatments had a distinct effect. However, no interpretable results were observed between the different levels of both treatments.