Abstract: A complementary S-matrix code modulation scheme was designed for digital micromirror spectrometer. The theoretical analysis proved that the complementary S matrix itself had good properties: it could improve for abouttimes of S matrix in respect of noise improvement. It was proved that this scheme could reduce the noise of stray light and dark current in implementing process by detailed deduction and analysis on noise-improvement theory of complementary S matrix through modeling on spectral signatures. When this scheme was applied in DMD spectrometer for experimental verification. The results demonstrate that the 63 order complementary S matrix coding scheme improved for 1.69 times compared with same-order S-matrix coding scheme in signal-to-noise ratio, which is identical with the theoretical analysis.