Co(Ti1-xZrx)Nb2O8 microwave dielectric ceramics were synthesized via the conventional solid-state reaction route. The dependence of microwave dielectric properties on the crystal structure was discussed. The phase transitions were analyzed using X-ray powder diffraction, Raman spectroscopy, and transmission electron microscopy. A series of composition-induced phase transitions were confirmed via the sequence: tetragonal rutile structure→coexistence of rutile and wolframite phase→monoclinic wolframite structure. For the Co(Ti1-xZrx)Nb2O8 compounds, Zr substitutions from 0 to 1 led to a decrease in the εr from 62.4 to 23.8. In contrast to εr, Q×f increased considerably, which was explained in terms of packing fraction. The τf was correlated with oxygen octahedral distortion and B-site bond valence. A near zero τf of 4.4ppm/°C was obtained in the CoTi0.4Zr0.6Nb2O8 ceramics with an εr of 29.9 and a high Q×f of 72,833GHz.