A previous study found that a crude Perilla seed polysaccharide (PFSP) fraction exhibited obviously antitumor activity; however, the structural characterization and antitumor properties of this polysaccharide remain unclear. In this study, the PFSP was extracted and purified via combined column chromatography, and the structure of a single polysaccharide fraction was characterized by methylation, IC, GC-MS, NMR, and AFM. The results demonstrated that the efficient antitumor polysaccharide fraction PFSP-2-1 was screened from PFSP with a relative molecular weight of 8.81 × 106 Da. The primary structure of the PFSP main chain was →1)-Araf-(5→, →1,3)-Galp-(6→, →1)-Galp-(6→, →1,3)-Araf-(5→ and →1)-Xylp-(4→, and that of the side chains was →1)-Arap, →1,3)-Galp-(6→, →1)-Araf and →1)-Glcp-(4→, →1)-Galp-(3→ and →1)-Glcp, leading to a three-dimensional helical structure. CCK-8 experiments revealed that PFSP-2-1 significantly inhibited the growth of human hepatocellular carcinoma cells in vitro (p < 0.05), and its inhibitory effect positively correlation with the concentration of PFSP-2-1, and when the concentration of PFSP-2-1 was 1600 µg/mL, it showed the highest inhabitation rate on three hepatocellular carcinoma cells (HepG-2, Hep3b, and SK-Hep-1), for which the survival rates of HepG-2, Hep3b, and SK-Hep-1 were 53.34%, 70.33%, and 71.06%. This study clearly elucidated the structure and antitumor activity of PFSP-2-1, which lays a theoretical foundation for revealing the molecular mechanism of antitumor activity of Perilla seed polysaccharides and provides an important theoretical basis for the development of high-value Perilla.