A stationary phase for the separation of C60 and C70 was prepared by modifying zirconia-magnesia composites with 2,4,6-trinitrophenol. The modified composite was characterized by using elemental analysis, diffused reflectance Fourier transform infrared spectroscopy and specific surface area. The effects of the toluene content in toluene-cyclohexane mobile phase and the column temperature on the separation of C60 and C70 were examined. Meanwhile, the separation of fullerenes including 3% high fullerenes was investigated at the temperature of 348 K using pure toluene as the mobile phase. The results showed that the stationary phase of 2,4,6-trinitrophenol-modified zirconia-magnesia composite exhibits advantage in the separation of C60 and C70, and strong temperature dependence. The retention times of C60 and C70 and their separation factor on the stationary phase increase with the increase of the column temperature. The stationary phase is a potential packing material for separation of fullerenes in preparative scale.