Sugar reduction and restriction have become one of the most urgent health demands as the number of obese people increases globally. Sugar substitutes (mainly classified into sugar alcohols, natural sweeteners, and artificial sweeteners) have been widely used in food processing as alternatives to sugar for their low energy and high sweetness. Thus, the classification, metabolism pathways, advantages, applications, and human health effects of sugar substitutes, their effects on human health were introduced, and the relationships between sugar substitutes and obesity, diabetes, intestinal microbes, hypertension, and all-cause mortality were emphatically summarized in this paper. Generally, long-term high intake of sugar substitutes is associated with adverse health outcomes such as elevated blood pressure, higher risks of diabetes, cancer, and increased all-cause mortality. Meanwhile, sugar alcohols and natural sweeteners are more likely to associate with beneficial effects on human gut microbial diversity, while artificial sweeteners associate with imbalance of gut microbiota based on available evidence. Current published research focuses on single sugar substitute exposure with varied health effects, while nearly half of commercial sugar substitute products contain two or more sugar substitutes. The effects of exposure to multiple sugar substitutes on human health are not clear yet, so further strengthening the relevant epidemiological and molecular mechanism research is necessary.