This study introduces a refined approach for more accurately estimating radiation doses to alimentary tract organs in nuclear medicine, by utilizing the ICRP pediatric and adult mesh-type reference computational phantoms (MRCPs) that improved the anatomical representation of these organs. Our initial step involved compiling a comprehensive dataset of electron Specific Absorbed Fractions (SAFs) for all source-target pairs of alimentary tract organs in both adult and pediatric phantoms, calculating SAFs for all cases in the present study only except those computed in the previous study for certain pediatric phantom cases. Subsequently, we determined S values for 1252 radionuclides, facilitating dosimetry applications. The consistency of target and source masses for alimentary tract organs in the MRCPs with the reference values in ICRP Publication 89 led to noticeable differences in SAF, S values, and consequently, absorbed dose coefficients when compared to the stylized models in ICRP Publication 100. Notably, the S value ratios (MRCP/stylized) for selected radionuclides—11C, 18F, 68Ga, and 131I—ranged from 0.41 to 7.60. Particularly for therapeutic 131I-iodide in thyroid cancer, the use of MRCPs resulted in up to 1.49 times higher absorbed dose coefficients for the colon than those derived from stylized models, while the stomach dose coefficients decreased by a factor of 0.72. The application of our findings promises enhanced, more realistic dosimetry for alimentary tract organs, especially beneficial for radiopharmaceuticals likely to accumulate within these organs.