It is an important subject to improve the temperature coefficient of resonant frequency (tf) and thermal conductivity (k) of microwave dielectric ceramics without reducing the Qf value. Ordered domain engineering was applied to realize the above objectives in Ba(Mg1/3Ta2/3)O3 ceramics. With the increasing ordering degree from 0.835 to 0.897, optimized Qf value was obtained. Meanwhile, near zero tf from 11.9 ppm/oC to 5.6 ppm/oC was achieved, together with increased k from 5.5 W m-1 K-1 to 7.6 W m-1 K-1, and enhanced dielectric strength from 801 kV/cm to 921 kV/cm. The noticeable ordered domain structure with large ordered domains (~100 nm) and low energy domain boundaries was revealed in Ba(Mg1/3Ta2/3)O3. The consequent weakened phonon scattering rises the thermal conductivity. The increased bond covalency and oxygen distortion in ceramics with higher ordering degree were suggested as cause of enlarged band gap, which enhanced the dielectric strength. The reduced tf is dominated by the less “rattling” space of the cations in the ordered state by inducing more positive te. The reduced tf, optimized thermal conductivity and Qf value in the present work indicate the ordered domain engineering could open up a new direction for the optimization of microwave dielectric ceramics.