The paper presents a study on the development and application of zirconium-based metal-organic frameworks (Zr-MOFs) supported titanium (Ti) single-atom catalysts (SACs). The research focuses on how the phase of Zr-MOFs influences the properties and catalytic performance of the Ti SACs. For the first time, it effectively outlines the significance of phase engineering in enhancing the performance of SACs. A new hexagonal close-packed (hcp) phase-engineered Zr-MOF designed to support and stabilize Ti single atoms. The resulting Ti-hcp Zr-MOF bipyridyl (bpy) SAC is effectively stabilized by organic linkers via robust nitrogen-metal interactions, preventing aggregation. Notably, Ti-hcp Zr-MOF(bpy) demonstrates superior catalytic performance compared to the conventional face-centered cubic (fcc) Zr-MOF(bpy)-supported Ti SAC in (trans)esterification reactions and biodiesel synthesis. Ti-hcp Zr-MOF(bpy) exhibits higher surface energy and a larger surface area than Ti-fcc Zr-MOF(bpy), which can improve the distribution and maximize the number of active sites. Moreover, DFT calculations reveal optimized adsorption free energies for intermediates and a reduced energy barrier for the transesterification of benzyl alcohol and ethyl acetate catalyzed by Ti-hcp Zr-MOF(bpy). This work provides valuable insights for the precise construction of highly active SACs.