Background Intravoxel incoherent motion diffusion-weighted imaging (IVIM-DWI) can distinguish the false diffusion generated by microvascular blood flow from the true water molecule diffusion. Purpose To investigate the correlation between IVIM-DWI parameters and angiogenic markers such as the microvessel density and vascular endothelial growth factor (VEGF) expression in the murine embryonal rhabdomyosarcoma model. Material and Methods The murine embryonal rhabdomyosarcoma model was produced by subcutaneously injecting 107 human embryonal rhabdomyosarcoma cells into the right back of nude mice. The apparent diffusion coefficient (ADC), pseudo-diffusion coefficient (D*), true diffusion coefficient (D), and perfusion fraction (f) were obtained from 22 mice models using IVIM-DWI with b-values of 0, 50, 100, 150, 200, 400, 600, 800, 1000, and 1200 s/mm2. The microvessel density and VEGF expression were obtained by histologic examination. We then compared the correlation between IVIM-DWI parameters and microvessel density and VEGF expression. Results The average ADC, D*, D, and f values were 1.05 ± 0.27 × 10−3 mm2/s, 6.19 ± 1.78 × 10−3 mm2/s, 0.69 ± 0.09 ×10−3 mm2/s, and 17.68 ± 8.41 (%), respectively. There was moderate positive correlation between D* value and microvessel density and VEGF expression (r = 0.484, P = 0.023; r = 0.511, P = 0.015). However, there was no significant correlation between ADC, D, and f values and microvessel density and VEGF expression. Conclusion The D* value from IVIM-DWI may be used to evaluate tumor angiogenesis in the murine embryonal rhabdomyosarcoma model.