The controllable formation of a built‐in electric field (IEF) can effectively separate photogenerated electrons and holes and optimize the band structure of a material, thus improving its photocatalytic performance. Here, a novel type of defective metal‐organic framework (MOF), i.e., an MIL‐125(Ti)@Ti‐Ce‐MOF yolk‐shell Z‐scheme heterojunction, is synthesized using a simple ion‐etching‐coupled reconstruction method. By controlling the concentration of ligand defects within the MOF heterojunction, the strength of the IEF within the heterojunction can be effectively regulated. Moreover, the experimental and theoretical results demonstrated that ligand defects within the Z‐scheme heterojunction structure can enhance the efficiency of photogenerated carrier separation and improve the transport capacity by regulating the IEF. The photocatalytic tetracycline (TC) degradation performance of the resultant MIL‐125(Ti)@Ti‐Ce‐MOF yolk‐shell heterojunction is ≈52.5‐ and 5.5‐fold higher than those of Ti‐Ce‐MOF and MIL‐125(Ti), respectively, indicating the efficient spatial charge separation due to the enhanced IEF. This study reveals the precise control of the IEF over the MIL‐125(Ti)@Ti‐Ce‐MOF yolk‐shell Z‐scheme heterojunction, elucidating the relationship between the IEF and ligand defect concentration and promoting the photocatalytic performances of MOF@MOF‐based catalysts via density functional theory and related experiments.