Ganyong (Canna edulis) is a local starch source with a naturally high starch content (about 88.10%), yet its industrial use remains limited because native ganyong starch is prone to gelatinization, retrogradation, and syneresis. This study modified native ganyong starch (NGS) through cross-linking using a combination of sodium tripolyphosphate (STPP) and sodium trimetaphosphate (STMP) to improve its physicochemical stability. A Central Composite Design (CCD) under Response Surface Methodology (RSM) was used to evaluate the effects of the STPP:STMP ratio and cross-linking temperature on swelling power, solubility, syneresis, Water Binding Capacity (WBC), and Oil Absorption Capacity (OAC). The STPP:STMP ratio was the most dominant factor: increasing the ratio decreased swelling power, solubility, syneresis, and WBC, while increasing OAC, consistent with the formation of distarch phosphate cross-links. The optimum condition was obtained at an STPP:STMP ratio of 19:1 and a temperature of 45.907°C, with a desirability value of 0.928. FTIR analysis showed no new ester group formation, confirming that the modification was physical in nature; SEM showed that granule morphology remained largely intact; and XRD confirmed that the B-type crystalline pattern was retained despite a change in the degree of crystallinity. Overall, cross-linking improved the thermal and structural stability of ganyong starch without altering its fundamental crystal structure.