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Metal-organic frameworks (MOFs) with new topologies and enhanced properties can be obtained by connecting metal-organic layers (MOLs) using multifunctional linkers. However, new topologies constructed by this method using linear-shaped ligands have not yet been explored. Herein, we present the design of NUT-123, by incorporating a near-linear perylene diimide (PDI) derivate, PDI-CH3-COOH into the preselected zirconium-based MOLs. 3D electron diffraction confirms the successful construction of a novel topology in NUT-123. Furthermore, the uniformly dispersed PDI groups within the structure confer enhanced photocatalytic capability while effectively circumventing the self-aggregation of PDI-CH3-COOH. NUT-123 exhibits enhanced efficiency and selectivity in sulfide oxidation and demonstrates excellent substrate compatibility, achieving 100% conversion of various organic sulfides. Mechanistic studies indicate that the formation of sulfoxides is facilitated by concurrent electron and energy transfer. This work fills the gap in constructing a new topology by connecting MOLs with linear-shaped linkers and provides a photocatalyst for selective sulfide oxidation.