The main objective of this research was to monitor variety in the content of Bacillus subtilis 10160 during solid‐state fermentation (SSF) of rapeseed meal by near infrared (NIR) spectroscopy and chemometrics. Observations showed the coefficient of determination (R2) value was 0.9401 and root‐mean‐square deviation was 0.639 log (CFU/g) for viable cell content by synergies between four intervals 5,203.003–5,600.267, 5,604.124–6,001.388, 6,807.487–7,204.751 and 8,411.972–8,809.235 cm−1. The determination coefficient of prediction (Rp2) and root‐mean‐square deviation of prediction in an external validation set could reach 0.9532 and 0.628 log (CFU/g) by the viable B. subtilis model. These findings suggest that rapid detection of B. subtilis in SSF is achieved by the combination of synergy interval partial least squares and NIR spectroscopy.