The application of nanotechnology in pesticide loading can improve the uptake and transportation behavior in plants, which helps to increase the utilization efficiency of pesticides. In this work, prochloraz-loading mesoporous silica nanoparticles were prepared to study the translocation, distribution and degradation of the target pesticide in cucumber plants. Fluorescein isothiocyanate labeled nanoparticles were used to track the distribution of the carriers in plants. Four hours after the treatment on the leaves, the nanoparticles could be found in the leaves, stem, petioles and roots. Fourteen days later the concentration levels of prochloraz and its metabolite were measured in different parts of cucumber using high performance liquid chromatography tandem mass spectrometry. Compared to the conventional suspension concentrate, prochloraz-loaded mesoporous silica nanoparticles had almost the same fungicidal activity, and they tend to be absorbed by cucumber plants with a better deposition performance. The final residue levels of prochloraz in cucumbers were lower than the maximum residue levels, which indicated the low risk of p-MSN application on the plant.