Metal–organic frameworks (MOFs), as a new type of nanomaterial, have been rapidly developed and widely applied in the environmental area. However, the algae removal efficiency of MOFs, the effect of metal ions and organic ligands contained in MOFs and the stability of MOFs in water need further study. Based on the characteristics of algae, five types of MOFs, which were Cu-MOF-74, Zn-MOF-74, ZIF-8, Ag/AgCl@ZIF-8 and MIL-125(Ti) were synthesized and characterized by X-ray diffractometer (XRD), field emission scanning electron microscope (FESEM), and X-ray photoelectron spectroscopy (XPS). The effect of MOFs on the growth of Microcystis aeruginosa was comparatively studied, and the inhibition mechanism of MOFs on algae as well as the stability of MOFs was explored. Results showed that all of the as-synthetic MOFs had superior stability in water, and the order of stability of MOFs followed the order MIL-125(Ti) > Cu-MOF-74 > Ag/AgCl@ZIF-8 > ZIF-8 > Zn-MOF-74. The types of metal ions and organic ligands doped in MOFs have grade affected the inhibitory efficiency on the algae: containing Cu²⁺ and Ag⁺ ions, MOFs had more significant inhibitory capacity to algae than those containing Zn²⁺ ions; meanwhile, compared with MOFs which are assembled with 2,5-dihydroxyterephthalic acid (DHTA) organic ligands, MOFs containing 2-methylimidazole (GC) organic contributed to the removal of algae significantly. The order of inhibitory effects of algae by five MOFs follows the order Cu-MOF-74 > Ag/AgCl@ZIF-8 > ZIF-8 > Zn-MOF-74 > MIL-125(Ti). The physiological characteristics of algal cells were changed after being treated with different concentrations of Cu-MOF-74. Once the concentration of Cu-MOF-74 reached 1 mg L⁻¹, the algal cells began to be inhibited, the relative inhibition rate of algal cells at 120 h was over 400%, and the inhibition process fitted pseudo-second-order kinetic model well. The Cu²⁺ released by Cu-MOF-74 that the concentration higher than 1 mg L⁻¹ would lead to the destruction of algae cell morphology and the loss of cell integrity, causing cell contents to be partially released into the water, promoting the accumulation and precipitation of algal cells which were destabilizing already to achieve the purpose of inhibition of algae. In summary, MOFs can be used to inhibit the growth of cyanobacteria and have a promising application prospect.