Till now, the transformation of amorphous flocs formed during the hydrolysis stage of coagulation has not been fully addressed. In this work, by using a conventional coagulant (alum), the transformation process was explored by observing the interactions between O3 and the amorphous alum flocs formed during flocculation at neutral pH. It was found that O3 promoted the transition of the in-situ formed alum flocs from tetrahedral Al (Al(O)4) to octahedral Al (Al(O)6) structures, through an accelerated dehydroxylation process, and therefore facilitated the crystallization process to form boehmite. During this process, the surface functional groups of amorphous Al flocs (triple bondAl–H2O and triple bondAl–OH) were observed to take part in the O3 catalytic oxidation with the generation of hydroxyl radicals (radical dotOH). This synergistic effect significantly favored the performance of the subsequent dual-membrane (UF-NF) process in terms of both fouling alleviation (1.78 and 1.60 times higher flux of UF and NF, respectively) and final effluent quality improvement, including the reduction in disinfection byproduct (DBP) formation potential (48.1% and 22.4% lower generation of total trihalomethanes and total haloacetic acid, respectively) and the corresponding calculated toxicity. The results obtained here provide a greater understanding of the transformation of amorphous Al flocs formed during flocculation with O3, and valuable information regarding its practical application in membrane filtration process with greater treatment performance.