Spermidine and spermine are special polyamines in organisms, and produced in vivo by putrescine and S-adenosylmethionine catalyzed by a variety of enzymes. Spermidine and spermine possess multiple amino groups, and are closely related to cell division, growth and survival. Spermidine and spermine alkaloids are widely distributed in plants, bacteria and marine organisms, and can be divided into macrocyclic and open chain according to the skeletons. Spermidine and spermine alkaloids exhibited numerous pharmacological effects such as anti-inflammatory, antibiotics, anti-tumor, anti-Alzheimer and anti-virus. However, up to now, there are few systematic reviews on spermidine and spermine alkaloids. In this review, based on the number of atoms in the ring, we summarized the distributions and pharmacological effects of spermidine and spermine alkaloids. Spermidine and spermine alkaloids have special chemophenetic significances in the plant kingdom, especially the macrocyclic spermidine and spermine alkaloids. Spermidine alkaloids are much more abundant in nature than spermine alkaloids. The pharmacological activities of the open chain spermidine and spermine alkaloids are studied in depth. Polycyclic guanidine spermidine alkaloids, isolated from marine sponge, exhibit great potential in various cancer cells. However, pharmacological studies of macrocyclic spermidine and spermine alkaloids are scarce. Synthesis is an effective way to get more spermidine and spermine alkaloids and their analogues for further study.