Our research aimed to cost-effectively enhance apigenin content in Chrysanthemum indicum L. extract using soybeans combined with a deep eutectic solvent. First, various deep eutectic solvents were investigated for the extraction of apigenin, followed by soybean treatment to increase aglycon levels. Combining single factor experiments with response surface methodology and optimization algorithms (genetic algorithm and particle swarm optimization), the optimal conditions were also determined. The results revealed that choline chloride-propylene glycol emerged as the optimal solvent. The optimized treatment conditions involved a temperature of 54 °C, a time of 2 h, and the addition of 3 mL of soybean extract, yielding an apigenin content of 3.380 ± 0.031 mg/g - a remarkable eightfold increase compared to the initial extract. The computational study suggested that the deep eutectic solvent may play an important role in stabilizing β-glucosidase in soybeans. However, further research is needed to scale up and fully elucidate soybean's mechanism.