Abstract Liquid organic scintillators are widely used in non-destructive analysis, which plays an important role in nuclear disarmament verification. This paper focused on studying the neutron-gamma discrimination technology in the fast neutron multiplicity measuring counter based on BC501A liquid scintillation detector. First, the charge comparison method, the zero-crossing time method and the rise time method were compared via the Geant4 and Matlab algorithm, and the result shows that charge comparison has the highest Figure of Merit. Then, a neutron-gamma discrimination system based on the six-probe fast neutron multiplicity counter was built and tested with a conclusion that the mean value of Figure of merit is 1.08, which verify the satisfactory neutron-gamma discriminating capability of the system. Finally, for the uranium samples, the mass are detected by fast neutron multiplicity counter, and the enrichment are measured by the characteristic gamma-ray signals using the system. The experimental results are in good agreement with the actual data.