Abstract: To overcome the application limitations of natural jatropha starch, such as susceptibility to aging and poor solubility and stability, this study employed composite enzyme (EMD) synergistic medium grinding treatment (M-EMD), high-pressure homogenization treatment (H-EMD), nano-precipitation (N-EMD) modification techniques to enhance oilseed starch. The modified starch was then incorporated into starch-based double emulsion systems to evaluate its effects on interfacial tension, stability, and the in vitro digestion of lycopene-loaded emulsions. Results indicated that the modification effects of different synergistic modification methods on starch were significantly different. N-EMD treatment demonstrated optimal performance, yielding starch particles with the smallest size (0.797 μm), the most uniform distribution (PDI=0.19), the highest surface negative charge (Zeta potential=−70 mV), and the strongest hydrophilicity (contact angle=23.1°). Structural analysis revealed that both H-EMD and N-EMD treatments effectively induced starch molecular restructuring. The double emulsion droplets constructed from N-EMD starch were fine, uniform, and structurally regular, exhibiting the highest lycopene encapsulation efficiency (88%) and loading capacity (66%). During storage, this emulsion exhibited the optimal physical stability and minimal lipid oxidation. In simulated in vitro digestion, its free fatty acid release rate (45%) and Lyc bioavailability (48%) significantly surpassed other groups. In conclusion, enzyme-assisted nano-precipitation (N-EMD) represented the most effective strategy for optimizing oil palm starch properties and constructing efficient starch-based delivery systems. This study pioneers new pathways for high-value utilization of jatropha starch and provides theoretical foundations and technical references for developing high-performance food-grade delivery carriers for bioactive compounds.