<p>Polar skyrmions exhibit extraordinary potential for next-generation functional electronics due to their topologically protected chirality and strong interactions under external stimuli. While polar skyrmions in ferroelectric systems can form highly ordered spatial structures known as skyrmion crystal, their configurations are typically simple hexagonal or tetragonal lattices, limiting the diversity of local skyrmion environments and hindering their selective manipulation. Here, through phase-field simulations, we theoretically report an electric-field-induced honeycomb lattice in PbTiO₃ thin films that constitutes a complex skyrmion crystal structure. This configuration is stabilized via simulation conditions guided by comprehensive phase diagrams spanning temperature, film thickness, and external electric field. The phase diagrams of the polar lattice further reveal previously unreported phase transition pathways among topological phases mediated by polar skyrmion interactions. Moreover, the selective manipulation of the erasure and recovery of the sublattices in the honeycomb skyrmion crystal is achieved through an applied in-plane electric field that couples with the asymmetric deformation of skyrmions. These findings advance the understanding of inter-skyrmion interactions and introduce a new route based on complex lattice engineering for tailoring the functional properties of the skyrmion crystal for device applications.</p>