Based on embedded web server,a new design method for scientific grade COD data acquisition system is proposed. And the data acquisition system is realized on the basis of the ARM micro-processor, embedded Linux and the fiber transfers module. It has some advantages such as the high ability of anti-jamming and none restriction of transmission distance and so on. The experimental results show that the system can realize the long distance data acquisition for the scientific grade COD and the efficient data transfer. The data acquisition distance is longer than 100 m and the transfer rate is 8 MHz.