Polyoxymethylene dialkyl ethers, which can be blended into diesel fuels, have attracted increasing attentions due to their advantages for fuel additives. It can utilize bioethanol and biomass syngas, helping to achieve the carbon neutral target earlier. Polyoxymethylene diethyl ethers (PODEEn) synthesis requires efficient catalysts with high performance. In this work, the mesoporous acidic functional N-containing ZrNxOy catalysts were prepared with a Sol-Gel assisted solvothermal method. The acid nature and strength, morphology, crystalline structure and pore distribution of catalysts were characterized by fourier transform infrared (FT-IR) spectroscopy, pyridine-adsorption infrared spectra (Py-IR), scanning electron microscopy (SEM), Transmission electron microscopy (TEM), X-ray diffraction (XRD), thermogravimetric analysis/differential scanning calorimetry (TGA/DSC), N2 adsorption-desorption isotherm, X-ray photoelectron spectroscopy (XPS), temperature-programmed desorption of ammonia (NH3-TPD) etc, showing catalyst possessing crystalline-amorphous mixed domains with smaller defective tetragonal nanoparticles and mesopores. The catalysts were applied in PODEEn synthesis, showing excellent activity and selectivity under mild conditions. And the high trioxane (TOX) conversion of 93 % and excellent PODEE2−8 selectivity of 98 % can be achieved at 80 °C under atmospheric pressure owning to the superior properties.