Aiming at the problem that the concentration detection of Azotobacter chroococcum in microbial fertilizer suffers from time consuming and low automation level, a detecting method of Azotobacter chroococcum concentration based on microfluidic chip was proposed．A dedicated microfluidic chip with automatic sample injecting, dilution and cyclic voltammetry detection was designed, and the experiment platform based on microfluidic detection system was bulit. The optimum scan rate and feed rate of concentration detection in the microfluidic detection system were determined, and the performance index of the system was experimentally verified. Experiment results showed that, compared with plate counting method, the proposed method met the requirement of microbial fertilizer detection and realized rapid detection with increased automation.