Aiming at the problems of polarization of the measuring electrode and contamination of the measured solution in the traditional contact electrolyte solution conductivity measurement, a non-invasive double-coil electrolyte solution conductivity measurement system based on eddy current effect is proposed. Through the establishment of a finite element analysis model, the effects of excitation frequency and coil geometry parameters on the sensitivity of the measurement system are discussed in depth, which provides a theoretical basis for the design of the system probe as well as the error analysis. In the experimental part, the coil probe parameters are optimized, and the FPGA-based dual-coil differential-frequency type measurement system is built, which is capable of converting inductance changes into frequency changes and realizing digital signal output. The dual-coil consists of a detection coil and a reference coil, in which the detection coil is used to measure the measured solution, the reference coil is far away from the measured solution and is only affected by the environment, and the signals of the two are realized as differential outputs, which can eliminate external interference. Comparison experiments show that the system can effectively measure different conductivity solutions, which verifies the correctness of the simulation model. Further temperature and anti-interference experiments show that the dual-coil differential structure significantly enhances the anti-interference performance of the system while ensuring the measurement accuracy, and the overall error is controlled within 1.2%, which demonstrates the practicality and reliability of the system.