The incidence and mortality rate of liver cancer are on the rise worldwide and effective therapeutic strategies are needed. Previous studies demonstrated that exosomes and exosome-like nanoparticles (ELNs) have numerous biological activities including antioxidant, anti-tumor, and anti-inflammatory effects. In this study, ELNs were successfully isolated for the first time from Radix Polygoni Multiflori (RPM) juice by ultracentrifugation. This indicated that RPM-ELNs could be internalized by hepatoma cells effectively and inhibit their proliferation and migration in vitro. RNA sequencing and qPCR experiments were performed, and the results of bioinformatic analyses revealed that RPM-ELNs could globally regulate expression levels of numerous genes associated with cancer and the cell cycle. In addition, it showed that RPM-ELNs mainly target liver tissue of mice in vivo.