The invention discloses a treatment method of polygonatum cyrtonema seeds. The treatment method comprises the following steps of putting collected and harvested polygonatum cyrtonema fruit into a cool and ventilate position in a spreading placing way; thoroughly decomposing the polygonatum cyrtonema fruit in a natural state for 5 to 8 days; breaking the thoroughly decomposed polygonatum cyrtonema fruit through extrusion to obtain the polygonatum cyrtonema seeds with pulp; fermenting the obtained polygonatum cyrtonema seeds with the pulp for 2 to 3 days in the natural state; performing seed and pulp separation; performing rinsing by cleaning liquid to obtain the polygonatum cyrtonema seeds. The method solves the problems that an ordinary treatment method can cause the seed coat damage; the pulp removal on the seeds is incomplete; the time and the labor are wasted.