The isospin effects of isoscaling parameter α on the nucleon-nucleon cross section are investigated for two couples of central nuclear reactions 40C+ 40Ca with 60Ca + 40Ca and 112Sn+ 112Sn with 124Sn+ 124Sn within an isospin dependent quantum molecular dynamics. It is found that the isospin effect of isoscaling parameter α on the isospin dependent nucleon-nucleon cross section σmedNN(αm) compared with that on the isospin independent nucleon-nucleon cross sections σ1NN(αm) is very obvious. However, the isospin effect of isoscaling parameter α on σmedNN(αm) compared with that on the isospin independent nucleon-nucleon cross section σ2NN(αm) is small. The mechanisms for the above difference are investigated in detail.