The impact of phase separation behavior on the performance of hydrogels has always been the research focus. This study explored the relationship of “pH-microstructure-hydrogel properties” of phase-separated hydrogels composed of type-A gelatin (GE, 5 wt%) and hydroxypropyl starch (HPS, 3 wt%). The results revealed that changes in the microstructure of the hydrogel at different pHs significantly impacted the gel properties. At pH 4.00 and 11.00, phase separation occurred in the GE/HPS gel with a microstructure of HPS-in-GE. In particular, at pH 5.00, 6.00, 7.00, and 9.00, severe phase separation resulted in the separation of substantial aggregates of HPS and GE, resulting in a continuous phase structure. At pH 2.00 and 3.00, phase separation was suppressed, resulting in a homogeneous microstructure. Compared to the phase-separated gels at pH 4.00–11.00, the homogeneous systems at pH 2.00 and 3.00 displayed a synergistic effect with higher gel strength. Analysis of intermolecular forces in the GE/HPS gel indicated that hydrogen bonding was the primary interaction force. Furthermore, the addition of GE/HPS into hawthorn jelly at about pH 3.00 effectively preserved the structural appearance and exhibited higher levels of hardness, thus improving the sensory properties of hawthorn jelly. In summary, phase separation decreased the storage modulus of GE/HPS gel, but the compatibility of GE/HPS macromolecules exhibited synergistic effects at 2.00 and 3.00 and improved the hydrogel mechanical properties. This work provides some new insights for GE/HPS-based gel foods.