Following the sequential Osborne extraction procedure, the proteins of lotus seeds were classified. The secondary structures of albumin, globulin, prolamine and glutelin fractions were determined by Fourier transform infrared spectroscopy (FTIR). The FTIR images of amide Ⅰ and Ⅲ bands from the four protein fractions were analyzed using Fourier deconvolution and curve-fitting technique. The results showed that there were minor differences in every corresponding peak position and peak area percent of secondary structure between albumin and globulin as well as between prolamin and glutelin. But there were differences in every corresponding peak position between albumin (or globulin) and prolamin (or glutelin). Especially the area percents of the corresponding nonrandom structures (α-helix and β-sheet) of albumin and globulin were significantly larger than those of prolamin and glutelin. The contents of nonrandom structures of albumin and globulin extracted with 0.1 mol·L-1 NaCl solution were about 55% and those of prolamine and glutelin fractions were only at round 40%, indicating that the secondary structures of the salt-extraction protein were ordered and stable.