High level of aluminum content in Enteromorpha prolifera posed a growing threat to both its growth and human health. This study focused on exploring the factors, impacts, and process of removing aluminum from Enteromorpha prolifera using humic acid. The results showed that under experimental conditions of 0.0330 g·L-1 humic acid concentration, pH 3.80, 34 °C, and a duration of 40 min, the removal rate was up to 80.18%. The levels of major flavor components, proteins, and amino acids in Enteromorpha prolifera increased significantly after treatment, while polysaccharides and trace elements like calcium and magnesium decreased significantly. Infrared spectroscopy demonstrated that the main functional groups involved in binding with Al3+ during humic acid adsorption were hydroxyl, carboxyl, phenol, and other oxygen-containing groups. The adsorption process of Al3+ by humic acid was a spontaneous phenomenon divided into three key stages: fast adsorption, slow adsorption, and adsorption equilibrium, which resulted from both physical and chemical adsorption effects. This study provided a safe and efficient method in algae metal removal.