Here we demonstrate on the ultra-fast synthesis route for the preparation of highly ordered FDU-12 with a 3D mesoporous structure and large and tuneable pore diameters ranging from 9.31 to 19.14 nm using microwave irradiation technique at various reaction temperatures ranging from 100 to 250 °C. High-end techniques such as powder X-ray diffraction, N2 adsorption-desorption, 29Si magic angle spinning nuclear magnetic resonance spectroscopy, high resolution scanning electron microscopy (HRSEM) and high resolution transmission electron microscopy (HRTEM) were employed to characterise the structure and texture of prepared samples. The characterization results reveal that all the samples exhibit a 3D mesostructure with well-ordered pores and excellent textural properties. The high temperature microwave process not only allows the quick condensation of the silica precursors and formation of mesostructure within a short microwave reaction time but also plays a critical role in controlling the pore diameter and the textural parameters of samples. The pore diameter of samples increases from 9.31 to 19.14 nm with increasing the reaction temperature from 100 to 250 °C. Finally, the FDU-12 samples with ultra-large pore diameters were subjected for protein adsorption studies using lysozyme as an adsorbate. The influence of pore diameter, surface area and pore volume on the adsorption potential of FDU-12 samples has been investigated. Among the materials studied, the FDU-12 with the largest diameter showed the highest adsorption capacity for lysozyme molecules. These results confirm that the pore diameter of FDU-12 is a vital parameter to control the adsorption capacity of FDU-12 materials with a 3D porous structure as the 3D structure with a large pore diameter permits an easy diffusion of the large protein molecules inside the mesostructure and allows the access to the interior part of porous channels.