After transgenic cotton residues incubated in soil 430 d, the contents and structural characteristics of soil humus fractions, fulvic acid, humic acid and humin were measured by potassium dichromate titrimetric method and Fourier transform infrared spectroscopy. The results showed that all soil humus fractions increased after the degradation of cotton residues, and the most relative increase was with humin and the least was with fulvic acid. Compared to their near-isogenic non-transgenic cottons, soil humus content for transgenic Bt cotton residue decreased, and that forr transgenic Bt+CpTI cotton Z41 was approximate, but that for transgenic Bt+CpTI cotton SGK321 increased. Infrared spectroscopy of fulvic acid, humic acid and humin showed the addition of cotton residue decreased the content of oxygenous groups, and increased the alkyl and amide groups. There were differences in the speed to form soil humus among three transgenic cottons. Transgenic Bt cotton was slower than its counterpart, transgenic Bt+CpTI cotton Z41 was approximate to its counterpart, but transgenic Bt+CpTI cotton SGK321 was faster than its counterpart.