Sophisticated chemical processes widely observed in biological cells require precise apportionment regulation of building units, which inspires researchers to develop tailorable architectures with controllable heterogeneity for replication, recognition and information storage. However, it remains a substantial challenge to endow multivariate materials with internal sequences and controllable apportionments. Herein, we introduce a novel strategy to manipulate the apportionment of functional groups in multivariate metal-organic frameworks (MTV-MOFs) by preincorporating interlocked linkers into framework materials. As a proof of concept, the imprinted apportionment of functional groups within ZIF-8 was achieved by exchanging imine-based linker templates with original linkers initially. The removal of linker fragments by hydrolysis can be achieved via postsynthetic labilization, leading to the formation of architectures with controlled heterogeneity. The distributions of functional groups in the resulting imprinted MOFs can be tuned by judicious control of the interlocked chain length, which was further analyzed by computational methods. This work provides synthetic tools for precise control of pore environment and functionality sequences inside multi-component materials.