Polymalic acid (PMA) is a biodegradable polymer produced by the polyextremotolerant fungi Aureobasidium pullulans and has been shown to have potential applications in environmental fields. In this work, a high PMA yield mutant FJ-D2 was screened from T-DNA-based mutant libraries and showed a 12.9% increase in PMA titers, which was attributed to decreased the expression of a glycosyltransferase gene (celA), resulting in a 39.5% reduction in cellulose biosynthesis. Untreated waste xylose mother liquor (WXML), an environmental waste generated from the xylitol industry, can be directly used as an economical substrate for PMA production. Using batch-fermentation of FJ-D2, the PMA titer of 57.1 +/- 0.02g/L was produced in a 5-L fermentor, with the highest MA yield of 0.77g/g mixed sugar. Furthermore, compared with ethylenediaminetetraacetic acid (EDTA), PMA had a comparable cadmium (Cd) removal efficiency (88.7% for EDTA versus 86.0% for PMA), which was not found in the monomer of L-malic acid (MA) monomers. These findings indicated that PMA was an environmentally friendly and biodegradable chelator for soil remediation. Moreover, our results provided an economically competitive process for PMA production from renewable environmental wastes.