Objective To evaluate the effects of radioactive impurity nuclides in ⁹⁰Y glass microsphere on therapeutic dose during radioembolization of pancreatic cancer. To provide a reference for correction of the dose calculated for individuals with different pancreatic tumors. Methods In this study, the radioactive impurity nuclide composition of ⁹⁰Y glass microsphere samples was analyzed to determine the source term of Monte Carlo calculation. Then, according to the PET/CT medical imaging data of pancreatic cancer patients, the three-dimensional modeling software Solidworks 2020 was used to construct the real and personalized digital human digestive system model of pancreatic cancer patients at a resolution showing the vascular distribution in pancreas and tumor. Finally, the Monte Carlo program GATE 8.2 was used to simulate the three-dimensional radiation dose fields of radioactive impurity nuclides ⁹¹Y and ⁶⁵Zn from ⁹⁰Y glass microspheres in various tissues and organs. The three-dimensional dose fields were visualized to analyze the influence of radioactive impurity nuclides on therapeutic dose. Results The three-dimensional radiation dose fields of ⁹¹Y and ⁶⁵Zn from ⁹⁰Y glass microspheres demonstrated two dose extreme points. The maximum dose value of ⁹¹Y to tissue was 0.272 mGy and the maximum dose value of ⁶⁵Zn to tissue was 9.34 μGy, with average statistical errors of less than 3.2%. Conclusion The impact of radioactive impurity nuclides ⁹¹Y and ⁶⁵Zn in 90Y glass microsphere sample on therapeutic dose is minimal and can be neglected.