The direct incorporation of guest crystals into another type of host crystals during the formation of the latter is technically challenging due to the large difference in surface energy for different crystalline components. Nevertheless, we herein demonstrate that metal-organic frameworks (MOFs, UiO-66-NH2 as a model guest crystal) after postsynthetic modification with poly(methacrylic acid) can be efficiently incorporated into calcite single crystals, forming a unique composite structure where the MOF crystals are uniformly distributed throughout the whole calcite host crystals. Remarkably, such MOF@calcite composite crystals exhibit superior performance in fluoride removal compared with the MOF or calcite alone. Moreover, this incorporation strategy is general as it can be extended to other guest particles. In principle, this study opens up a versatile avenue for the rational design and preparation of a wide range of hybrid functional materials with controllable compositions and enhanced physicochemical properties.