Background: The current clinical practice to manage kidney stone requires knowledge of the stone composition. However, it is often difficult to determine the actual stone composition before a stone is operatively removed from the patient. Dual-energy computed tomography (DECT) can predict urinary stone composition, but it is not widely adopted. The purpose of the study was to investigate the use of a second-generation DECT with tin or stannum (Sn) filter for characterising the kidney stones composition. Methods: Thirty-three kidney stones were scanned ex vivo using a dual-source (DS)DECT scanner with dual-energy (DE) mode of 80/140 kVp with and without 4 mm Sn filtration. DE ratio was calculated to determine the kidney stones composition (uric acid, calcium oxalate, calcium phosphate and cystine). The median DE ratio of the stones was compared using Wilcoxon signed rank test and the results were further correlated with semi-quantitative Fourier transform infrared (FTIR) spectroscopy analysis using Kendall’s Tau test with P < 0.05 deemed to be statistically significant. Results: Second-generation DS-DECT could significantly discriminate the stones composition with and without Sn filtration (P < 0.001). The median DE ratio of uric acid, calcium oxalate and cystine stones were significantly higher with Sn filtration than those without filtration (P < 0.05). DECT results revealed significant correlation with FTIR spectroscopy analysis (r = 0.716, P < 0.001). DECT with Sn filtration showed increased performance (100% sensitivity, 0% specificity) than those without filtration (48.5% sensitivity, 0% specificity) in the detection of the kidney stone subtypes. Conclusion: In the second-generation DECT with additional Sn filtration, DECT has shown a significant performance in characterising and discriminating the kidney stone composition. This may improve diagnostic and therapy management in kidney stones cases.