Ba4Nd9.33Ti18-zAl4z/3O54 (BNT-A, 0 ≤ z ≤ 2) and Ba4Nd9.33+z/3Ti18-zAlzO54 (BNT-AN, 0 ≤ z ≤ 2) ceramics were prepared by solid state method, and the effects of the two doping methods on microwave dielectric properties were compared. As the doping amount z increased, the relative dielectric constant (εr) and the temperature coefficient of resonant frequency (τf) values of the ceramics decreased, and the quality factor (Q, usually expressed by Q×f, where f is the resonant frequency) of the ceramics obviously increased when z ≤ 1.5. With the same z value, the εr and Q×f values of Al/Nd co-doped ceramics are both higher than those of Al-doped ceramics. Rietveld refinement, Raman spectroscopy and thermally stimulated depolarization current (TSDC) technique were applied to clarify the relationship among the structure, defects and microwave dielectric properties. It is shown that the Q×f values of those ceramics were closely related to the strength of the A-site cation vibration and the concentration of oxygen vacancies (B). Excellent microwave dielectric properties of εr = 72.2, Q×f = 16480 GHz, and τf = +14.3 ppm/℃ were achieved in BNT-AN ceramics with z = 1.25.