Glycoalkaloids (GAs) are a class of special secondary metabolites found in plants. Studies have found that they have a wide range of pharmacological activities, such as antiviral, antifungal and anticancer properties, with significant potential for development and utilization value. At present, alkaloid glucosides mainly fall into two categories: indole alkaloid glucosides and steroid alkaloid glucosides (SGAs). Additionally, there are small amounts of quinolines, isoquinolines, isoguanines and other alkaloids. At present, only a few of the GAs have been found, which is inconsistent with the diversity of alkaloids. Additionally, only a few GAs have been isolated and identified. This paper reviews the natural alkaloid glycosides from the perspectives of structural classification and pharmacological activity. It analyzes the reasons for the limited number of isolated components and proposes a rational separation method based on the literature. To provide references for the separation, identification and bioactivity of glycoalkaloids.