The problem of cyanobacteria blooms during potable water production has generated wide concern. Ferrate(VI) serving as a pre-oxidation tactic was first applied to enhance conventional Fe(II) coagulation for Microcystis aeruginosa-laden water treatment at lab scale. Results demonstrated that ferrate(VI) pre-oxidation could successfully destabilize algae cells through destroying the protective organic layer. The residual ferrate(VI) together with post-added Fe(II) could provoke a comproportionation reaction, where large amounts of Fe hydrolyzates [Fe(OH)3] are formed. The in-situ Fe(OH)3 with abundant reactive surface is responsible for the promotion of flocs growth by facilitating the clustering and cross-linking of algal organic matters (AOM) and cyanobacteria cells, simultaneously resulting in satisfactory reductions in OD680, turbidity and UV254. Overdose of ferrate(VI) could cause severe cell destruction along with the release of intracellular organic matter (IOM), which may impair the water quality by increasing the concentration of dissolved organic carbon (DOC) and the disinfection by-products formation potential (DBPFP). Meanwhile, considering the Fe residual in settled water, the optimal ferrate(VI) dose (20 µM) and Fe(II) dose (80 µM) were proposed. Besides, the synergistic effect of both the degradation by ferrate(VI) and the adsorption by in-situ Fe(OH)3 contributed to the removal of DOC and Microcystin-LR. This study suggests that ferrate(VI) might be a potential candidate for pre-treatment to assist Fe(II) coagulation when addressing algae-laden water.