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Probing in-medium nucleon-nucleon (NN) cross section σ(1N)N(α) in heavy ion collisions has been investigated by means of the isospin-depeadent quantum molecular dynamics (IQMD) with the isospin-and momentum-dependent interaction (IMDI(τ)). It is found that there are the very obvious medium effect and the sensitive isospin-dependence of nuclear stopping R on the in-medium NN cross section σ(1N)N(α) in the nuclear reactions induced by halo-neutron projectile and the same-mass stable projectile. However, R induced by the neutron-halo projectile is obviously lower than that induced by the corresponding stable projectile. In particular, there is a very obvious dependence of R on the medium effect of σ(1N)N(α) in the whole beam energy region for the above two kinds of projectiles. Therefore, the comparison between the results of R’s in the reactions induced by the neutron-halo projectile and the corresponding same-mass stable projectile is a more favourable probe for extracting the information of σ(1N)N(α) because of adding a new judgement.