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Three typical algorithms of Pauli blocking in the quantum molecular dynamicstype models are investigated in the nuclear matter, the nucleus and the heavyion collisions. The calculations in nuclear matter show that the blockingratios obtained with the three algorithms are underestimated 13-25\% comparedto the analytical values of blocking ratios. For the finite nucleus, thespurious collisions occur around the surface of the nucleus owing to thedefects of Pauli blocking algorithms. In the simulations of heavy ioncollisions, the uncertainty of stopping power from different Pauli blockingalgorithms is less than 5\%. Furthermore, the in-medium effects ofnucleon-nucleon ($NN$) cross sections on the nuclear stopping power arediscussed. Our results show that the transport models calculations with free$NN$ cross sections result in the stopping power decreasing with the beamenergy at the beam energy less than 300 MeV/u. To increase or decrease thevalues of stopping power, an enhanced or suppressed model dependent in-medium$NN$ cross section is required.

Effects of Pauli blocking and in-medium nucleon-nucleon cross sections on the stopping power at low-intermediate energy heavy ion collisions