l-malic acid is a versatile compound having extensive applications across food, pharmaceutical, medical, and chemical industries while its production from microbial fermentation offers sustainable advantages including renewable feedstocks and environmental friendliness. However, a major challenge faced by microbial l-malic acid production is acid-induced pH drop during the fermentation process, requiring excessive neutralizers (e.g., CaCO3) that increase costs and environmental burdens greatly. In this study, we firstly made an engineered Aspergillus nidulans strain as a production chassis through metabolic engineering by overexpression of fructose-6-phosphate kinase gene (pfkA) combined with deletion of pyruvate decarboxylase gene (pdcA) so that the titer of l-malic acid was increased by 20.3 %. Secondly, overexpression of glucose transporter gene (mstE) further boosted production to the highest reported shake-flask titer (44.3 g/L) for A. nidulans. Moreover, acid-tolerant isolates capable of growth at pH 2.8 has been successfully obtained by adaptive laboratory evolution in aforementioned engineered strains. They achieved 75 % neutralizer reduction (just adding 10 g/L CaCO3) while maintaining original titers. Whole-genome sequencing comparison identified mutations in gene (ANIA_04699) encoding a protein with a topoisomerase II associated PAT I domain happened in acid-tolerance isolates. Functional validation via engineered point-mutants confirmed mutations of the gene (ANIA_04699) as a key acid-tolerance determinant, contributes a major role enabling CaCO3 reduction without titer loss. Meanwhile, phylogenetic studies showed there are about 71-75 % homology across selected Aspergillus spp. suggesting high conservation and broad applicability. Function prediction analysis based on previous verified PAT I domains imply that mutations of this topoisomerase II-Like protein might be tolerant to DNA damage induced by low pH environment. This work establishes A. nidulans as a platform for low-pH organic acid production and identifies topoisomerase II variants as new targeted candidates for acid tolerance engineering.