Low-loss tungsten—bronze microwave dielectric ceramics are dielectric materials with potential application value for miniaturized dielectric filters and antennas in the fifth-generation (5G) communication technology. In this work, a novel Al/Nd co-doping method of Ba4Nd9.33Ti18O54 (BNT) ceramics with a chemical formula of Ba4Nd9.33+z/3Ti18−zAlzO54 (BNT—AN, 0 ≼ z ≼ 2) was proposed to improve the dielectric properties through structural and defect modulation. Together with Al-doped ceramics (Ba4Nd9.33Ti18−zAl4z/3O54, BNT—A, 0 ≼ z ≼ 2) for comparison, the ceramics were prepared by a solid state method. It is found that Al/Nd co-doping method has a significant effect on improving the dielectric properties compared with Al doping. As the doping amount z increased, the relative dielectric constant (εr) and the temperature coefficient of resonant frequency (τf) of the ceramics decreased, and the Q×f values of the ceramics obviously increased when z ≼ 1.5. Excellent microwave dielectric properties of εr = 72.2, Q×f = 16,480 GHz, and τf = +14.3 ppm/°C were achieved in BNT—AN ceramics with z = 1.25. Raman spectroscopy and thermally stimulated depolarization current (TSDC) technique were firstly combined to analyze the structures and defects in microwave dielectric ceramics. It is shown that the improvement on Q×f values was originated from the decrease in the strength of the A-site cation vibration and the concentration of oxygen vacancies $$\text{V}_\text{O}^{^{ \cdot \cdot }}$$, demonstrating the effect and mechanism underlying for structural and defect modulation on the performance improvement of microwave dielectric ceramics.