β-1,3-Glucan oligosaccharides produced by enzymatic hydrolysis of β-1,3-glucans are of great interest, because they possess biological functionalities such as regulating intestinal health, improving immunity and anti-tumor. A significant qualification for the industrial production of glucan oligosaccharides is β-1,3-glucanase with high catalytic ability. These enzymes are widely present in fungi, bacteria, plants and invertebrates, they are separated into glycoside hydrolase families 3, 5, 16, 17, 55, 64, 72, 81, 128 and 132. This report presents the research progress on the construction and expression of β-1,3-glucanases in Pichia pastoris and Escherichia coli from different microorganisms. Culture conditions and strategies to improve enzyme activity in these hosts are summarized. The application of β-1,3-glucanases in different β-1,3-glucans (curdlan, scleroglucan, laminarin, and schizophyllan) degradation and their hydrolysate analysis are reviewed. This review provides an important reference for further modification and utilization of microbial β-1,3-glucanases in large-scale production of multi-functional oligosaccharides.