An advanced microbe chip testing method was put forward, and a new digital imaging scanning system for testing biochips was developed. A novel CCD scanning system with laser induced fluorescence for biochip detection was proposed, with a high numerical aperture NA=0.72 for collecting fluorescence, long working distance 3.22 mm and high sensitivity less than 1 fluorescent molecule /μm2. Microbe chip was designed and tested by the above novel CCD scanning system, which provided a whole solution scheme for efficient food safty inspection. An example of testing escherichia coli and xanthomonas campestris was shown and proved the stability and creditability of the system. The experimental results obtained by the developed digital imaging scanning system indicated the same correct identification of microbe as the commercial confocal scanner.