Bacillus cereus is a kind of common food-borne pathogen that can cause vomiting and diarrhea shortly after ingestion. The spectroscopy properties of Bacillus cereus were measured using the infrared reflectance spectroscopy, which was a nondestructive technology. The influence of Bacillus cereus concentration on the spectroscopy was explored based on the two-dimensional (2D) correlation spectroscopy method. The results showed that some functional groups of capsule in pure Bacillus cereus culture, such as carboxyl, protein amide I and amide II, C-H methyl and methylene could induced some self-correlation peaks near 1592 cm−1, 1652 cm−1, 1512 cm−1 and 1412 cm−1 respectively. Some functional groups of spore, such as COO- group and C-H bond could induced some self-correlation peaks near 1348 cm−1, 1616 cm−1 and 1592 cm−1 respectively. In milk sample, the functional groups of capsule and spore could induced some self-correlation peaks too. The infrared spectroscopy combined with 2D correlation spectroscopy analysis method could be a effective method for the Bacillus cereus detection.