Abstract: In view of the luminous flux of the miniature spectrometer is low, and is not conducive to the weak signal detection and analysis, a near-infrared spectrometer based on Hadamard transform was designed. In order to compensate the energy loss of the spectrometer used S matrix coding, a complementary S matrix coding was proposed. Complementary S matrix for energy enhancement theory was derived in detail through the establishment of the coordinate system that digital micro-mirror as the core. Finally, some experiments were made by using spectrometer and the result verified the theory. The results show that with the increase of the coding order of scanning, measured light energy is reduced, while smaller changes of the measured spectral energy of S matrix. The light energy of the S matrix combination measurements than single slit scanning measurements has been significantly enhanced，while still lost nearly half of the spectral energy. The complementary S matrix coding scheme based on S matrix can compensate the losing energy of micro-mirror which is off state. When the spectrum signal is extremely weak，the spectrogram of single slit scan is submerged in the noise signal, while the spectrogram measured by S matrix and complementary S is still can recognised. And in terms of noise suppression, complementary S matrix is better than the S matrix. These results are consistent with the theoretical analysis.