Mesoporous silica nanoparticles (MSNs) can be used as carriers to deliver pesticides into plants, which is considered to be one method of improving the efficacy of pesticide usage in agricultural production. In the present work, MSNs with an average diameter of 258.1 nm were synthesized and loaded with Fenoxanil. The structure of the nanocarriers was observed by scanning electron microscopy. The loading content of Fenoxanil-loaded MSNs was investigated. After rice plants in a hydroponic system were treated with loaded MSNs, the concentrations of Fenoxanil in different samples were determined using high-performance liquid chromatography–tandem mass spectrometry. The results suggested that rice plants can absorb MSNs from water through their roots, and the dosage has almost no effect on the distribution of Fenoxanil in rice plants. The application of pesticide-loaded nanoparticles in a hydroponic system poses a low risk of Fenoxanil accumulation in rice.