Anthraquinones are compounds of high medicinal value in many plants. Based on their good protein binding affinity, foam fractionation was attempted to separate them using proteins in the aqueous extract of Semen Cassiae as collectors. Firstly, the interaction between anthraquinones and Semen Cassiae proteins has been analyzed by the Stem−Volmer equation with physcion as a standard. The results show that physcion had good interaction with the proteins via hydrophobic forces. More importantly, the proteins effectively assisted the foam fractionation of several anthraquinones including aurantio-obtusifolin, aloe-emodin, rhein, emodin, chrysophanol, and physcion. On this basis, a two-stage foam fractionation technology was developed for process intensification using a foam fractionation with vertical sieve trays (VSTs). VSTs, initial feed concentration of total anthraquinones, temperature, volumetric air flow rate and pore diameter of gas distributor had significant effects on enrichment ratio and recovery yield of anthraquinones. Under suitable conditions, the enrichment ratio of total anthraquinones reached 47.0 ± 4.5 with a concentration of 939 ± 94 mg/L in the foamate while their total recovery percentage reached more than 47.7%. In addition, foam fractionation also increased the purity and hydroxyl radical scavenging activity of total anthraquinones. The results had significant implications for the separation of anthraquinones from Semen Cassiae.