α-1,3-Glucan is one of the main polysaccharides in the cell wall of <italic>Aspergillus nidulans</italic>. We previously revealed that it plays a role in hyphal aggregation in liquid culture, and that its molecular mass (MM) in an <italic>agsA</italic>-overexpressing (<italic>agsA</italic>^{<italic>OE</italic>}) strain was larger than that in an <italic>agsB</italic>-overexpressing (<italic>agsB</italic>^{<italic>OE</italic>}) strain. The mechanism that regulates its MM is poorly understood. Although the gene <italic>amyD</italic>, which encodes glycosylphosphatidylinositol (GPI)-anchored α-amylase (AmyD), is involved in the biosynthesis of α-1,3-glucan in <italic>A</italic>. <italic>nidulans</italic>, how it regulates this biosynthesis remains unclear. Here we constructed strains with disrupted <italic>amyD</italic> (Δ<italic>amyD</italic>) or overexpressed <italic>amyD</italic> (<italic>amyD</italic>^{<italic>OE</italic>}) in the genetic background of the ABPU1 (wild-type), <italic>agsA</italic>^{<italic>OE</italic>}, or <italic>agsB</italic>^{<italic>OE</italic>} strain, and characterized the chemical structure of α-1,3-glucans in the cell wall of each strain, focusing on their MM. The MM of α-1,3-glucan from the <italic>agsB</italic>^{<italic>OE</italic>}<italic>amyD</italic>^{<italic>OE</italic>} strain was smaller than that in the parental <italic>agsB</italic>^{<italic>OE</italic>} strain. In addition, the MM of α-1,3-glucan from the <italic>agsA</italic>^{<italic>OE</italic>} Δ<italic>amyD</italic> strain was greater than that in the <italic>agsA</italic>^{<italic>OE</italic>} strain. These results suggest that AmyD is involved in decreasing the MM of α-1,3-glucan. We also found that the C-terminal GPI-anchoring region is important for these functions.