In strong electromagnetic field environment, it is difficult for the traditional data acquisition system to carry out effective and reliable data acquisition accurately.To deal this situation, a variety of electromagnetic shielding options have been taken, including designing electromagnetic shield to shield the frontend interference of the acquisition system, building fiberoptic Ethernet to ensure the purity of transmission data, etc. In addition, taking FPGA as the main chip of data acquisition systems and using DSP for data compression and transmission. The results show that the whole system is more stable and reliable, and the antiinterference ability has been greatly improved, and the precision and transmission speed of the data acquisition have also been improved, which act as effective solution to the data collection and transferring under complex electromagnetic environment.