The subjects of this study were recruited from Zha Shui and An Kang counties in the Qinba mountain region located in Middle-west China. The present study discussed the relationship between the variations of GDI1 with the children NSMR and their intelligence levels. The case-control association analysis method was used to analyze the association between the polymorphisms of two functional SNPs (rs2276462 and rs11549300) located in splicing site of the seventh exon and the eighth exon respectively, with NSMR and their different intelligence levels. It does not find out the polymorphism of rs2276462, because of its conservation. The results of case-control analysis indicated that, no association between the rs11549300 polymorphisms and children NSMR (P >0.05), but its polymorphisms may be related to intelligence levels of children in Qinba region (P =0.03). And a further work should be done to verify the conclusion of this study using the more genetic markers of GDI1 in a larger sample.