The applications of nanoparticles suffer from their extremely small size and intrinsic trend of agglomeration. Rearranging nanoparticles to form micro-sized nanoaggregates (MNAs) with increased size, ordered structure, as well as controllable size, shape, and morphology is a crucial step in various fields of science and technology to maintain the unique characteristics of nanoparticles while obtaining greatly enhanced or new performances at the microscale. The structure of MNAs prominently affects their functionality, which is determined by the arrangement of nanoparticles and the interaction between primary particles. Several methods have been proposed to prepare the MNAs, in which spray-drying technology stands out considering the feasibility, scalability for industry, cost, and efficiency. Forced assembly of nanoparticles through spray-drying under tunable process parameters yields diverse physical properties and structural arrangements of nanoparticles of the MNAs, they therefore exhibit enormous potential in a wide range of application fields. This review presents the construction and applications of spray-dried MNAs. The factors that influence the size, morphology, and structure of the MNAs are discussed in detail. In addition, the outstanding application performance resulting from the tightly packed nanoparticles in regular-shaped MNAs obtained by the spray-drying process is illustrated.