Over the past decades, the presence of pharmaceutical emerging contaminants in water bodies is receiving increasing attention due to the high concentration detected from wastewater effluent. Water systems contain a wide range of components coexisting together, which increases the difficulty of removing pollutants from the water. In order to achieve selective photodegradation and to enhance the photocatalytic activity of the photocatalyst on emerging contaminants, a Zr-based metal-organic framework (MOF), termed VNU-1 (VNU represents Vietnam National University) constructed with ditopic linker 1,4-bis(2-[4-carboxyphenyl]ethynyl)benzene (H₂CPEB), with enlarged pore size and ameliorated optical properties, was synthesized and applied in this study. When compared to UiO-66 MOFs, which only had 30% photodegradation of sulfamethoxazole, VNU-1 had 7.5 times higher adsorption and reached 100% photodegradation in 10 min. The tailored pore size of VNU-1 resulted in size-selective properties between small-molecule antibiotics and big-molecule humic acid, and VNU-1 maintained high photodegradation performance after 5 cycles. Based on the toxicity test and the scavenger test, the products after photodegradation had no toxic effect on V. fischeri bacteria, and the superoxide radical (·O₂^-) and holes (h⁺) generated from VNU-1 dominated the photodegradation reaction. These results demonstrate that VNU-1 is a promising photocatalyst and provide a new insight for developing MOF photocatalyst to remove emerging contaminants in the wastewater systems.