Based on the potential of microbial fermentation in the sustainable and environmentally friendly production of L-malic acid (L-MA), this study aims to investigate the effect of glycosylphosphatidylinositol (GPI)-anchored proteins (GPI-APs) on enhancing the stability of Aspergillus niger (A. niger) cell wall to increase L-MA production. Through experiments, we discovered and screened GPI2, a GPI-anchored cell surface glycoprotein, and confirmed for the first time that it has a promoting effect on L-MA, a metabolite of A. niger. This recombinant strain RG0098 that overexpressed gpi2 showed an increase in cell wall thickness and robustness, a decrease in intracellular reactive oxygen species (ROS) levels, which improved the antioxidant capacity. After 108h of fermentation, the production of L-MA reached 114.7 ± 2.12g/L, and the productivity was 1.06 ± 0.025g/L/h. The strain RG0098 has enhanced the productivity of L-MA by a notable margin of 49.7%. This study provides a sustainable and environmentally friendly pathway for the production of L-MA through microbial fermentation.