Increasing the complexity of hollow structures, in terms of chemical composition and shell architecture, is highly desirable for both fundamental studies and realization of various functionalities. Starting with metal–organic frameworks (MOFs), we demonstrate a general approach toward the large-scale and facile synthesis of complex hollow microboxes via manipulation of the template-engaged reactions between the Prussian blue (PB) template and different alkaline substances. The reaction between PB microcubes with NaOH solution leads to the formation of Fe(OH)3 microboxes with controllable multishelled structure. In addition, PB microcubes will react with the conjugate bases of metal oxide based weak acids, generating multicompositional microboxes (Fe2O3/SnO2, Fe2O3/SiO2, Fe2O3/GeO2, Fe2O3/Al2O3, and Fe2O3/B2O3), which consist of uniformly dispersed oxides/hydroxides of iron and another designed element. Such complex hollow structures and atomically integrated multiple compositions might bring the usual physiochemical properties. As an example, we demonstrate that these complex hollow microboxes, especially the Fe2O3/SnO2 composite microboxes, exhibit remarkable electrochemical performance as anode materials for lithium ion batteries.