Aiming at long signal acquisition time, low flux, bad signal-to-noise ratio and low intelligence in coloration biochip reader, a new kind of rapid device with high flux was developed. The device consisted of hardware system and software system. It used a charge-coupled device (CCD) as the photoelectric sensor elements and obtained the biochip microarray image. The device integrated the embedded operating system based on i.MX6 chip. The microarray image processing, data analysis and result output were achieved through the code information of the software chip. Experiments with the standard grayscale sheet and standard format chip were carried out. The results showed that the maximum measurement error was less than 0.1%, the value of R2 was 98.7%, and the value of CV was 1.096 1%. The comparison results of 200 samples showed that detection performance of the proposed device was better than that of the same kind of marketed equipment.