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Nuclear medicine treatment requires patient-specific dose assessment as treatment plan reference. Voxelized dose results can give three-dimensional dose distribution. The conventional MIRD method assumes that the source is uniformly distributed within the organ, and the calculated dose results in an organ-averaged dose. In this study, based on molecular imaging data, the non-uniform distribution of the source term within the organ was obtained, and the voxel-level dose distribution was calculated for nuclear medicine patients using the following method. With accurate quantitative analyze of 131I SPECT images and CT images of patients, voxel S-value method and direct Monte Carlo (MC) method were used to calculate voxel-level dose distribution in nuclear medicine patients. The voxel S-factor is defined as the average absorbed dose of each radioactive decay in the source voxel to the target voxel, both of which are contained in an infinite homogeneous tissue. The voxel S-value is calculated to evaluate the dose of multiple surrounding source voxels to the target voxel. The three-dimensional dose distribution is calculated based on the source distribution obtained from the SPECT images. The MC simulation was processed based on the source distribution obtained from SPECT images and CT images. The HU value of each voxel in the patient’s body was obtained from the CT images, and the density value of each voxel was further obtained. The material of each voxel was divided according to the density to construct the voxel phantom. The voxel-level activity distribution was obtained based on the SPECT images to construct the source term distribution model. The MC simulation based on CT images was used to count the energy deposition of each voxel to obtain the accurate voxel-level dose distribution in the patient’s body. A 400x speedup was achieved using GPU MC simulation. The results of the S-value method and the MC method show a maximum difference of over 40% in the lung area. Voxel-level dose simulation can obtain the dose distribution in sub-organ and tumor, which provides a valuable reference for precision treatment of clinical nuclear medicine. The S-factor method can quickly give the dose distribution of patients, but this method ignores the tissue inhomogeneity, and the dose calculation results are not accurate in tissues and organs with large density differences, such as lung and bone, etc. The MC voxelized simulation can accurately give the dose distribution in patients, which is important for the accurate assessment of clinical dose in nuclear medicine.