An organic matter detection system based on hydrogen flame ionization detection method is designed. The working principle of the system is introduced firstly, and then the structural design of the system is optimized based on the principle. According to the reaction conditions of the system, the control circuit of the system is designed. In view of the weak detection signal and wide dynamic range of the system, a current detection circuit with switchable range is designed by using the method of transimpedance amplification, which realizes a wide range of micro-current detection. The performance of the system is quantified by methane standard gas, and it is shown that the relative standard deviation of standard sample repeatability measurement is less than 2%, and the linear correlation coefficient is greater than 0.99.