Magnetic nanoparticles (MNPs) bear many intriguing properties such as superparamagnetism, high specific surface area, remarkable colloidal stability and biocompatibility, which evoke great interest and desire of exploration in biomedical applications. For the use in the complicated physiological environment, MNPs are still being developed to have the enhanced performances and down-to-earth practicality. Engineering of MNPs into hierarchical structures is thus proposed to create a new family of magnetic materials, magnetic colloidal supraparticles (MCSPs), which exhibit collective properties and unique nanomaterial characters. From a biomedical point of view, applicability of MCSPs is somewhat more distinctive in contrast to their primary MNPs, because MCSPs are amenable to modulation of secondary structure, promotion of magnetic responsiveness and ease of function design. As a result, MCSPs have been subject to intense researches in recent years, with the aim to develop outstanding composite materials for biomedical applications. In this review, we embark on an overview of foundational topics that detail the design and fabrication of MCSPs by evaporation-induced emulsion and solvothermal techniques, and continue with a guideline for modification of MCSPs with inorganic oxides and organic polymers. Particular focus is then placed on the biomedical applications of modified MCSPs. Many examples illustrate the latest progress in design of MCSP-based microspheres for magnetic resonance imaging, targeted drug delivery, sensing, and harvesting of peptides/proteins. After these detailed accounts, the current challenges and future development of researches and applications are discussed as a conclusion to the review.