In today’s society, the rapid development of science and technology requires the detection of weak current signals in many fields of scientific research. The research of its detection technology plays a very important role in promoting the development of science and technology. Considering that the weak current signal has strong background noise, it is easy to be submerged, the detection is difficult, and the professional requirement is strong. This research proposes a weak current detection system based on an embedded system that can detect nan oampere-level weak currents. The detection system is mainly composed of signal conversion amplifier filter circuit module, signal acquisition circuit, STM32, FPGA, upper computer and so on. Through experimental inspection, the researched detection system has the advantages of high accuracy and good stability.