Commercial hard-type PZT piezoelectric ceramics mostly have dielectric constant below 1500. Pb(Ni1/3Nb2/3)O3 (PNN) effectively increases dielectric constant and overall piezoelectric properties of PZT since Luff et al. reported PNN-PZT system in 1974. Although most of them are soft-type PNN-PZT with dielectric loss higher than 0.01, several work investigated the improvement of B-site cation substitution such as Fe2O3 and NiO. MnO2 doping can enhance the sinterability of PNN-PZT ceramics by increasing oxygen vacancies via lower valence Mn substitution, but the in-depth research about microstructure and phase transition in MnO2-doped PNN–PZT was rarely found. This work employed low MnO2 additives to achieve higher dielectric constant, lower dielectric loss, and hardened piezoelectric properties in PNN– PZT system that were synthesized using the two-step columbite calcination method followed by the sintering at >1200°C. For the optimum MnO2 concentration, the work investigated Zr/Ti ratio effect on 0.13PNN-0.87PZT composition near the morphotropic phase boundary (MPB). The complex dielectric responses exhibited the tetragonal-rhombohedral phase transition below ferroelectric to paraelectric transition and their external bias field dependence. X-ray diffraction shows the evolution of tetragonal to rhombohedral structure with increasing the Zr/Ti ratios and test temperatures. Electron microscopy reveals the domain morphology transition from coarse and regular shapes to small and wavy morphology with increasing the Zr/Ti ratios. This work determined that the MPB of 0.13PNN-0.87PZT composition understudy is 50/50 for Zr/Ti and the optimum composition for higher dielectric constant is 49/51 for Zr/Ti.