Two series of polyurethane (PU) containing 2,2-bis(hydroxymethyl)propanoic acid (DMPA) and the grafted benzimidazole (BI) were prepared to compare their antifungal activities. The DMPA carboxyl group of BN series was completely ionized using a strong base (NaOH) and the DMPA carboxyl group of BT series was partly ionized by a weak base (trimethylamine). The BN series exhibited a faster decrease in maximum tensile strength and strain at break compared to the BT series. The fully ionized DMPA carboxyl group of BN series severely affected the thermal and mechanical properties. Finally, the BN series demonstrated a complete suppression of fungal growth (Chaetomium globosum) whereas unmodified PU and the BT series could not fully suppress the growth of fungi at the same BI content. Therefore, the complete ionization of DMPA carboxyl group played an important role in the antifungal activity.