The aim was to investigate the impact of PPARG and APOE gene single nucleotide polymorphisms (SNPs) and additional gene- gene interaction on late-onset Alzheimer's disease (LOAD) risk based on Chinese Han population. A total of 928 participants (466 males, 462 females), with a mean age of 81.3 +/- 16.4 years old, were included in the study, including 460 LOAD patients and 468 normal controls participants. Logistic regression was performed to investigate association between SNP and LOAD risk and generalized multifactor dimensionality reduction (GMDR) was used to analysis the gene-gene interaction. Logistic regression analysis showed that LOAD risk was significantly higher in carriers of G allele of the rs405509 polymorphism than those with AA (AG+ GG versus AA, adjusted OR (95%CI) =1.54(1.20-1.89), and higher in carriers of G allele of the rs1805192 polymorphism than those with CC (CG+ GG versus CC, adjusted OR (95%CI) =1.32(1.16-2.43). We also found that there was a potential gene-gene interaction between rs405509 and rs1805192. Participants with AG or GG of rs405509 and CG or GG of rs1805192 genotype have the highest AD risk, compared to participants with AA of rs405509 and CC of rs1805192 genotype, OR (95%CI) was 2.62(1.64 -3.58), after covariates adjustment. G allele of the rs405509 of APOE and G allele of the rs1805192 of PPAR G polymorphism were associated with increased LOAD risk, and participants with AG or GG of rs405509 and CG or GG of rs1805192 genotype have the highest AD risk.