Polyaluminum chloride modified clay (PAC-MC) is a safe and efficient red tide control agent that has been studied and applied worldwide. Although it is well known that the distribution of hydrolytic aluminum species in PAC affects its flocculation, little is known about the influence of particulars aluminum species on the microalgae removal efficiency of PAC-MC; this lack of knowledge creates a bottleneck in the development of more efficient MCs based on aluminum salts. The ferron method was used in this study to quantitatively analyze the distributions of and variations in different hydrolytic aluminum species during the process of microalgae removal by PAC-MC. The results showed that Ala, which made up 5%–20% of the total aluminum, and Alp, which made up 15%–55% of the total aluminum, significantly affected microalgae removal, with Pearson's correlation coefficients of 0.83 and 0.89, respectively. Most of the aluminum in the PAC-MC sank rapidly into the sediments, but the rate and velocity of settlement were affected by the dose of modified clay. The optimal dose of PAC-MC for precipitating microalgae was determined based on its aluminum profile. These results provide guidance for the precise application of PAC-MC in the control of harmful algal blooms.