A series of Mg-Zr composite oxide catalysts prepared by the hydrothermal process were used for the transesterification of glycerol (GL) with dimethyl carbonate (DMC) to produce glycerol carbonate (GC). The effects of the preparation method (co-precipitation, hydrothermal process) and Mg/Zr ratio on the catalytic performance were systematically investigated, and the deactivation of the catalyst was also explored. The Mg-Zr composite oxide catalysts were characterized by XRD, TEM, TPD, N2 adsorption-desorption, and XPS. The characterization results showed that compared with the co-precipitation process, the catalyst prepared by the hydrothermal process has a larger specific surface area, smaller grain size, and higher dispersion. Mg1Zr2-HT catalyst calcined at 600 °C in a nitrogen atmosphere exhibited the best catalytic performance. Under the conditions of reaction time of 90 min, reaction temperature of 90 °C, catalyst dosage of 3 wt% of GL, and GL/DMC molar ratio of 1/5, the GL conversion was 99% with 96.1% GC selectivity, and the yield of GC was 74.5% when it was reused for the fourth time.