Sulfated zirconia is used as solid acid catalyst in simultaneous (trans)esterification of low quality feedstock with free fatty acids for biodiesel production. However, its widespread application in catalytic reaction is limited by its framework and catalytic instability. Therefore, we prepared a stable sulfated zirconia catalyst with mesoporous structure and tetragonal phase nanocrystalline by using dioctyl dimethyl ammonium chloride as a template. The mesoporous sulfated zirconia shows more than 85% conversion of soybean oil after five recycle runs at 140 °C in both the transesterification and the simultaneous (trans)esterification. A comparison of physicochemical properties of the fresh and the reused catalysts shows that covalent sulfates combined with the sufficient of surface defective sites are the basis of the structural stability. With higher sulfate concentration, the ionic sulfate species absorbed on the low-index plane induce the production of abundant Brönsted acid sites, which are responsible for the activity in the transesterification or esterification, while the loss of these active sulfate species during the reaction is the intrinsic reason for the catalyst deactivation. Furthermore, simulation calculations confirm that position of two H+ affects the configurations of SO42− and the most stable 3-fold coordinated configuration sulfates play a dominant role in the formation of stronger Brönsted acid sites.