Harmful algal blooms (HABs) are a worldwide problem with numerous negative effects on water systems, which have prompted researchers to study applicable measures to inhibit and control them. This review summarized the current microorganisms-based methods or technologies aimed at controlling HABs. Based on their characteristics, these methods can be divided into two categories: methods based on single-species microorganisms and methods based on microbial aggregates, and four types: methods for rapid decrease of algal cells density (e.g., alga-bacterium and alga-fungus bioflocculation), inhibition of harmful algal growth, lysis of harmful algae (e.g. algicidal bacteria, fungi, and actinomycete), and methods based on microbial aggregates (periphytons and biofilms). An integrative process of "flocculation-lysis-degradation-nutrients regulation" is proposed to control HABs. This review not only offers a systematic understanding of HABs control technologies based on microorganisms but also elicits a re-thinking of HABs control based on microbial aggregates.