This study characterized the selective complex coacervation between hordein and pectin to confirm the selective binding behavior of different hordein components in order to develop a low-cost, readily scalable protein isolation method. Besides, the isolation of B-hordein was optimized and the adhesion properties of different components were also evaluated. The results demonstrated that B-hordein, the major component of hordein, preferentially bound to two types of pectin to form coacervates. High-methoxyl pectin (HMP) exhibited weaker binding affinity to B-hordein, as evidenced by the fact that the supernatant of the complex system contained a significant amount of B-hordein. In contrast, low-methoxyl pectin (LMP) showed stronger binding affinity to B-hordein. Protein spectrum analysis revealed that high-purity B-hordein could be obtained by collecting the coacervates from the Hordein/LMP_1:1 system. Adjusting the pH enabled the secondary separation of B-hordein from LMP in the coacervates, with a B-hordein recovery of 65.29%. Meanwhile, B-hordein-based composites exhibited the best adhesion performance. This study provides a theoretical foundation for promoting the development of protein isolation technologies.