In this study, hydrogel beads [SPI/HP-Fe (II)] were prepared by cross-linking soybean isolate protein (SPI) and hawthorn pectin (HP) with ferrous ions as a backbone, and the effects of ultrasound and Fe2+ concentration on the mechanical properties and the degree of cross-linking of internal molecules were investigated. The results of textural properties and water-holding capacity showed that moderate ultrasonic power and Fe2+ concentration significantly improved the stability and water-holding capacity of the hydrogel beads and enhanced the intermolecular interactions in the system. Scanning electron microscopy (SEM) confirmed that the hydrogel beads with 60% ultrasonic power and 8% Fe2+ concentration had a denser network. X-ray photoelectron spectroscopy (XPS) and atomic absorption experiments demonstrated that ferrous ions were successfully loaded into the hydrogel beads with an encapsulation efficiency of 82.5%. In addition, in vitro, simulated digestion experiments were performed to understand how the encapsulated Fe2+ is released from the hydrogel beads, absorbed, and utilized in the gastrointestinal environment. The success of the experiments demonstrated that the hydrogel beads were able to withstand harsh environments, ensuring the bioactivity of Fe2+ and improving its bioavailability. In conclusion, a novel and efficient ferrous ion delivery system was developed using SPI and HP, demonstrating the potential application of SPI/HP-Fe (II) hydrogel beads as an iron supplement to overcome the inefficiency of intake of conventional iron supplements.