Zn₃(Nb_1−xTa_x)₂O₈ (x = 0.02–0.10) ceramics were prepared via a solid-state reaction route and the dependence of their microwave dielectric properties on their structural characteristics were investigated. XRD patterns show that a single Zn₃Nb₂O₈ phase with layered crystal structures was formed in ceramic samples with 0.02 ≤ x ≤ 0.10. The Raman spectrum was used for the first time to analyze the vibrational phonon modes of the Zn₃Nb₂O₈ samples. Based on P–V–L dielectric theory, the intrinsic factors that influence the microwave dielectric properties were systematically investigated. According to the calculated results, the experimental dielectric constant had a close relationship with the theoretical dielectric constant. The Nb-site lattice energy was found to be a vital factor in explaining the change of the Q × f values. While the Nb-site bond energy increases, the |τ_f| value decreases which indicates that higher bond energy would result in a more stable system. This work presents a novel method to investigate the intrinsic factors that influence microwave dielectric properties.