In the daily diet, sweeteners play an indispensable role. Among them, sucrose, a widely occurring disaccharide in nature, is a commonly used sweetener. However, the intake of sucrose can cause a rapid increase in blood glucose, which leads to a number of health problems. Therefore, there is an urgent need for possible alternatives to sucrose. Currently, four naturally occurring sucrose isomers, trehalulose, turanose, leucrose, and isomaltulose are considered to be possible alternatives to sucrose due to their suitable sweetness, potential physiological benefits, and feasible production processes. This review covers the properties of these alternative sweeteners, including their structure, sweetness, hydrolysis rate, toxicology, and cariogenicity, and exhibits their potential applications in chronic diseases management, anti-inflammatory supplement, prebiotic dietary supplement, and stabilizing agent. The biosynthesis of these sucrose isomers using carbohydrate-active enzymes and their industrial production processes are also systematically summarized.