A facile DNA delivery method would greatly facilitate studies of plant functional genomics. However, plant cell walls limit the utilization of nanoparticles on plant research. Here, we employed functionalized mesoporous silica nanoparticles (MSNs) to develop a MSN-mediated plant transient gene expression system. In this system, MSNs served as carriers to deliver foreign DNA into intact Arabidopsis thaliana roots without the aid of mechanical force. Gene expression was detected in the epidermal layer and in the more inner cortical and endodermal root tissues by both fluorescence and antibody labeling. This is a novel alternative to the conventional gene-gun or ultrasonic methods. In addition, the parameters that affect the MSN uptake and the mechanism and subcellular distribution of particles were also analyzed. The present study may provide valuable information on the manipulation of functional nanoparticles in plants and have significant impact on plant biotechnology.