Microcapsule arrays attract a lot of interest due to their potential applications in sensing technology. A strategy for fabricating diverse microcapsule arrays through covalent linking is reported here. The self-assembly of microcapsules was directed by using a poly(allylamine hydrochloride) (PAH)-patterned template, which was created via microcontact printing. The microcapsules with PAH as the outermost layer were treated with glutaraldehyde and then covalently immobilized on the PAH regions, resulting in ordered microcapsule arrays. The arrays had a high density of capsules and the aggregate number in a pattern could be well controlled by adjusting the area of the PAH pattern. A single microcapsule array could be obtained if the diameter of the PAH region was smaller than that of the microcapsules. These covalently assembled arrays could survive through successive incubation in solutions of high ionic strength and extreme pHs. Such good stability ensures further treatments, such as chemical reactions and loading of functional substances.