The role of B-site ions of Bi0.5Na0.5TiO3 (BNT) on its complex phase transition remains unclear due to its polarization attributing to both Bi and Ti. In this paper, the phase transition of (Bi0.5Na0.5)0.94Ba0.06(Ti1−0.01b/4B0.01)O3 (BNT6BT) (B = Nb, Mn, Fe, and Cu) ceramics was modified by low-concentration donor doping (Nb) and acceptor doping (Mn, Fe, and Cu) in order to determine the origin of phase transition behavior. The phase structure, microstructure, local structure/lattice vibration, phase transition temperature, and dielectric properties of BNT6BT-Nb, Mn, Fe, and Cu ceramics were investigated. Results showed that all samples formed a single perovskite phase at room temperature, and donor (Nb) and acceptor (Mn, Fe, and Cu) doping can regulate the ratio of R3c and P4bm coexisting as nanoscale entities. The grains show polyhedral morphology, and average grain size lies between 1 and 2 μm. The Raman spectroscopy study shows that doping modification can change the phase transition temperature. The relation is in well agreement with the three different dielectric anomalies derived from the dielectric curves of εr versus T. Low concentration of cation (Nb, Mn, Fe, and Cu) doping can tailor the dielectric permittivity, depolarization temperature, and phase transition temperature of BNT6BT. All samples exhibit a large dielectric constant and good frequency stability.