Abstract For the first time, the effect of gemini based twin-tail and conventional surfactant on tungsten oxide nanostructures and their efficacy for the elimination of the organic pollutant is studied. The tungsten oxide nanostructures were synthesized by a simple hydrothermal route in the presence of C14TAB and gemini based twin-tail surfactant. The impact of using these special shape and size directing agents for the synthesis of nanostructures was observed in the form of different shapes and sizes. The tungsten oxide web of chains type nanostructure was obtained using C14TAB in comparison to the cube shaped nanoparticles through twin-tail surfactant. On contrary, the twin-tail surfactant provides sustainable and controlled growth of cube shape nanoparticles of size ~ 15 nm nearly half of the size ~ 35 nm obtained using conventional surfactant C14TAB, respectively. For the detailed structural features, the Williamson-Hall analysis method was implemented to find out the crystalline size and lattice strain of the prepared nanostructures. Owing to the strong quantum confinement effect, the WO3 cube shaped nanoparticles with an optical band gap of 2.69 eV of the prepared nanoparticles showed excellent photocatalytic efficacy toward organic pollutant (Fast green FCF) compared to the web of chain nanostructures with an optical band gap of 2.66 eV. The mechanism has been discussed in detail in the respective section. The ability of the prepared systems to decompose the organic pollutant (Fast green FCF) in water was tested under visible light irradiations. The percentage degradation was found to be 94% and 86% for WO3 cube shaped nanoparticles and WO3 web of chains, respectively. The simplicity of the fabrication method and the high photocatalytic performance of the systems can be promising in environmental applications to treat water pollution.