Aloe dairy products have occupied a certain market share, and the interaction between the small bioactive molecules contained in aloe and milk proteins during product processing profoundly affects the performance of dairy products. In this study, two typical and potentially dangerous bioactive small molecules of aloe, aloin (AA) and aloe-emodin (AE), were selected to investigate their interaction mechanism with β-lactoglobulin (β-La). Computer simulations showed that AA/AE had the potential to form complexes with β-La, and the β-La-AA system exhibited a stronger binding affinity than the β-La-AE system. Fluorescence analysis showed that the binding affinity values of AA to β-La at 298 K were deduced to be (4.184 ± 1.06) × 104 M−1, meaning medium-strength interactions, comparatively, AE to β-La was weaker, were deduced to be (3.15 ± 1.25) × 103 M−1. In addition, the thermodynamic analysis found that ΔH0 and ΔS0 were positive in both the β-La-AA system and the β-La-AE system, which implies that the main driving force for the combination of AA/AE and β-La to form the ground state complex is the hydrophobic force. The conformation changes in β-La brought about by binding to AA/AE may alter the properties and functions of the protein, such as surface hydrophobicity and oxidation resistance. Analysis shows that β-La is potentially present in whey as an AA/AE carrier during the production of aloe milk.