(Mg1/3Nb2/3)x(Zr0.5Ti0.5)1-xO2 (x = 0.00, 0.05, 0.10, 0.13, 0.15, and 0.20) systems without additives are fabricated by facile solid-state reaction method in the air atmosphere. The influence of (Mg1/3Nb2/3)4+ substitution on microwave dielectric properties of (Mg1/3Nb2/3)x(Zr0.5Ti0.5)1-xO2 ceramics is investigated systematically. The XRD results convey that the doping ion ((Mg1/3Nb2/3)4+) should occupy (Zr0.5Ti0.5)4+ site throughout the composition. An appropriate amount of (Mg1/3Nb2/3)4+ tremendously increases the temperature stability and reduces the microwave dielectric loss of the ZrTiO4 ceramic. In addition, to further investigate the dielectric loss mechanism, high-resolution Raman mapping is used to characterize residual stresses at the grain level. The result justifies that there is non-uniform residual stress in the ceramic, which is closely related to the anharmonic vibrations of the crystal lattice and the intrinsic loss of (Mg1/3Nb2/3)x(Zr0.5Ti0.5)1-xO2 ceramics. Meanwhile, the annealing approach is applied for reducing the intrinsic loss and further improving the Q × f value. Ultimately, the optimum microwave dielectric properties with τf ∼0.8 ppm/°C, high ϵr ∼40.9 and Q × f ∼40,217 GHz are obtained in annealed (Mg1/3Nb2/3)0.13(Zr0.5Ti0.5)0.87O2 ceramic, which suggests that it can be as one of the candidates exploiting for microwave devices in 5G wireless communication technology.