Abstract: ⁶⁴Cu is a crucial medical isotope enabling theranostics integration. The Medium and Long-Term Development Plan for Medical Isotopes (2021-2035), jointly issued by eight national ministries and commissions, explicitly points out its broad application prospects. At present, China’s capabilities in ⁶⁴Cu preparation and production still lag significantly behind the international state of the art. To optimize the design of isotope targets for ⁶⁴Cu production, this study employed the FLUKA code and adopted the control variable method to investigate the preparation of ⁶⁴Cu via proton beam bombardment of ⁶⁸Zn and ⁶⁴Ni targets. The research focused on multiple aspects, including irradiation energy (5~70 MeV), irradiation time (4~72 h), cooling time (0~390 h), and some relevant impurity nuclides generated during the preparation process. The results indicate that the optimal irradiation energies for the ⁶⁸Zn and ⁶⁴Ni targets are 35 MeV and 15 MeV, respectively; the optimal irradiation time for both targets is 36 h. The optimal cooling time for the ⁶⁸Zn target is 4 h, whereas the ⁶⁴Ni target requires immediate separation and purification after irradiation. During the irradiation of the ⁶⁸Zn target, ⁶⁷Cu is produced, which can form a nuclide pair with ⁶⁴Cu, a phenomenon not observed in the irradiation of the ⁶⁴Ni target. Both targets generate impurity nuclides such as ⁶⁵Ni, ³H and ⁵⁵Mn after irradiation. Considering comprehensive factors including accelerator performance requirements, ⁶⁴Cu yield, and radioactive nuclide purity, the ⁶⁴Ni target is superior to the ⁶⁸Zn target for ⁶⁴Cu preparation. The relevant research findings provide a reference for the design of isotope targets used in ⁶⁴Cu production via proton accelerators.