Contrast-enhanced imaging for choroidal malignant melanoma (CMM) is mostly limited to detecting metastatic tumors, possibly due to difficulties in fixing the eye position. We aimed to (1) validate the appropriateness of estimating iodine concentration based on dual-energy computed tomography (DECT) for CMM and optimize the calculation parameters for estimation, and (2) perform a primary clinical validation by assessing the ability of this technique to show changes in CMM after charged-particle radiation therapy. The accuracy of the optimized estimate (eIC_optimized) was compared to an estimate obtained by commercial software (eIC_commercial) by determining the difference from the ground truth. Then, eIC_optimized, tumor volume, and CT values (80 kVp, 140 kVp, and synthesized 120 kVp) were measured at pre-treatment and 3 months and 1.5–2 years after treatment. The difference from the ground truth was significantly smaller in eIC_optimized than in eIC_commercial (p < 0.01). Tumor volume, CT values, and eIC_optimized all decreased significantly at 1.5–2 years after treatment, but only eIC_commercial showed a significant reduction at 3 months after treatment (p < 0.01). eIC_optimized can quantify contrast enhancement in primary CMM lesions and has high sensitivity for detecting the response to charged-particle radiation therapy, making it potentially useful for treatment monitoring.