Vacancies are common in solid materials, but it remains a challenge to introduce them at specific locations with controlled distributions. Here we report the creation of ordered metal vacancies and linker vacancies in a cubic metal-organic framework (MOF) based on Zn(II) and pyrazolecarboxylic acid by removing a quarter of the metal ions and half of the linkers. The MOF with ordered vacancies shows increased pore size, thus allowing large dye molecules to fit in the pores. Furthermore, by filling the vacancies with new metals and new linkers, eight new single-crystalline MOFs with multicomponents in absolute order are introduced. The capability of performing stepwise elimination and addition reactions systematically in extended solids without destroying the structural integrity has generated complex MOF structures which otherwise cannot be made.