Combing the one-dimensional infrared spectroscopy (FTIR) technology with two order derivative spectrum technology, the growth change rule of bacillus cereus, the common food borne pathogenic bacteria, are analyzed without destruction, It is found that capsule, spore and other structures of bacillus cereus can be identified, based on the two order derivative spectra characteristic absorption peak. Observing shows the symmetric & anti symmetric carboxyl group stretching vibration absorption peaks near 1604.48 cm−1 and 1396.21 cm−1 gradually weaken from lag phase to the stable phase. With protein amide absorption peak near 1654.63 cm−1 tending to be stable in the three stages, the structural changes of cell capsule can be acknowledged. The DPA absorption peak near 1617.98 cm−1, 1384.64 cm−1, and 1560.13 cm−1 indicates the presence of bacillus, changing in three stages from lag phase to stable phase. Experiments show that FTIR can distinguish cells’ material structure, which lays a theoretical foundation for the related devices of fast detection for bacillus cereus.