Abstract: In the in vivo measurement for internal contamination, the detector count from the radionuclides deposited in organs other than the lung is neglected for lung counter. Besides, the monitored people have morphological deviation with the reference phantom in calibration. The organ-specific detection efficiency for ⁶⁵Zn and ⁶⁰Co nuclides was simulated with Monte Carlo code by using the Chinese adult male phantom library, and the total detection efficiency was calculated. The effect of organ-specific detection efficiency and total detection efficiency on virtual calibration was studied. The results show that the contribution of nuclides like ⁶⁵Zn in the organs other than the lung can not be neglected in the virtual calibration. The total detection efficiency of the lung counter for ⁶⁵Zn and ⁶⁰Co nuclides decreases with the increase of weight at the same height, and the decreased proportion for ⁶⁵Zn varies with the time after intaking. For each phantom, the total detection efficiency decreases with the increase of time. The results prove that the radionuclide biokinetic distribution and morphological variation have a great influence on the total detection efficiency of the lung counter, which varies with nuclides.