Three typical Pauli blocking algorithms in quantum molecular dynamics type models are investigated in the nuclear matter,the nucleus,and heavy ion collisions.In nuclear matter,the blocking ratios obtained with the three algorithms are underestimated by 13％-25％ compared to the corresponding analytical values.For a finite nuc-leus,spurious collisions occur around the surface of the nucleus owing to the defects of the Pauli blocking al-gorithms.In the simulations of heavy ion collisions,the uncertainty of stopping power arising from the different Pauli blocking algorithms is less than 5％.Furthermore,the in-medium effects of nucleon-nucleon (NN) cross sec-tions on the nuclear stopping power are discussed.Our results show that the transport model calculations with free NN cross sections result in the stopping power decreasing with beam energy when the beam energy is less than 300 MeV/u.To increase or decrease the values of the stopping power,the transport model calculations need enhanced or suppressed model dependent in-medium NN cross sections that are expected to be smaller than the true in-medium NN cross sections.