Distinct crystal phases of an oxide affect the configuration of surface atoms, which might further affect coordination with sulfate during sulfonation for the preparation of SO42−/MxOy type of acid catalyst. Herein, such an effect is investigated with zirconia of the tetragonal or monoclinic phase as the model catalysts. The results show that sulfonation inhibits the transformation of zirconia from the tetragonal phase to the monoclinic phase, whereas the varied phase of zirconia also affects the bonding patterns of sulfate species with zirconia in sulfonation. The sulfated zirconia of monoclinic phase contains more abundant acidic sites and more Brønsted acid sites than that of sulfated zirconia of tetragonal phase. Consequently, the sulfated zirconia of monoclinic phase is more active than the sulfated zirconia of tetragonal phase for the conversion of furfuryl alcohol in ethanol and conversion of fructose in dimethyl sulfoxide, achieving the yield of ethyl levulinate of 96.4% and a high yield of 5‐hydroxymethylfurfural. The sulfated zirconia is not stable in protic solvent due to the leaching of sulfur species and the change in configurations of the sulfate species and the zirconium species, but in the aprotic solvent, they show good stability and recyclability.