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<i>Allium</i> is a common functional vegetable with edible and medicinal value. <i>Allium</i> plants have a special spicy taste, so they are often used as food and seasoning in people’s diets. As a functional food, <i>Allium</i> also has abundant biological activities, some of which are used as drugs to treat diseases. By consuming <i>Allium</i> on a daily basis, people can receive active compounds of natural origin, thereby improving their health status and reducing the likelihood of disease. Steroidal saponins are important secondary metabolites of <i>Allium</i>, which are formed by the steroidal aglycone group and sugar. Steroidal saponins have various physiological activities, such as hypoglycemic, antiplatelet aggregation, anti-inflammatory, antitumor, antimicrobial, and enzyme activity inhibition, which is one of the key reasons why <i>Allium</i> has such significant health benefits. The structural diversity and rich biological activities of steroidal saponins make <i>Allium</i> important plants for both food and medicine. In this paper, the chemical structures, biological activities, and structure–activity relationships of steroidal saponins isolated from <i>Allium</i> are reviewed, and the biosynthetic pathways of some key compounds are proposed as well, to provide a molecular reference basis based on secondary metabolites for the health value of <i>Allium</i>.