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Background: In clinical practice, Preoperative differentiation between hepatocellular carcinoma and intrahepatic cholangiocarcinoma is challenging but critical for treatment decisions. Objective: This study investigated the discriminatory power of the stretched-exponential model and fractional-order calculus model parameters for hepatocellular carcinoma versus intrahepatic cholangiocarcinoma in orthotopic xenograft nude mice. Methods: Prototype orthotopic xenograft models of hepatocellular carcinoma and intrahepatic cholangiocarcinoma were developed using 20 nude mice divided into two groups and separately transplanted with MHCC97H and HUCCT1 cells. Readout-segmented diffusion-weighted imaging with multiple b-values (0–2000 s/mm2) was obtained using a 3.0-T magnetic resonance imaging scanner. The apparent diffusion coefficient was calculated using the mono-exponential model. The distributed diffusion coefficient and intravoxel water molecular diffusion heterogeneity (α) were calculated using the stretched-exponential model. The diffusion coefficient (D), fractional-order derivative in space (β), and spatial parameter (μ) were calculated using the fractional-order calculus model. The liver and tumor specimens of nude mice were immunostained after euthanasia to clarify the liver cancer type. Differences in diffusion-related parameters between the groups were evaluated using Mann–Whitney U-test and univariate logistic analysis. Receiver operating characteristic curves were used to assess the diagnostic efficacy of each parameter. P Results: α, D, and β were significant discriminators between the groups. The area under the curve for these three variables was 0.890, 0.830, and 0.870, respectively, with cutoff values of 0.491, 0.435, and 0.782, respectively. Conclusion: The stretched-exponential model parameters α and the fractional-order calculus model parameters D and β showed high diagnostic efficacy in discriminating intrahepatic cholangiocarcinoma from hepatocellular carcinoma in orthotopic xenograft nude mouse models. conclusion: The stretched-exponential model parameter α and the fractional-order calculus model parameters D and β showed high diagnostic efficacy in discriminating intrahepatic cholangiocarcinoma from hepatocellular carcinoma in orthotopic xenograft nude mouse models.