Abstract: The underwater natural neutron with different water depths from 1 m to 25 m in Yi Lake was measured by an underwater neutron measuring device which uses a spherical 3He proportional counter as the neutron sensitive component. Combining with some Monte Carlo simulations, the low energy natural neutron generation rate and fluence rate at different depths in Yi Lake were acquired. The results indicate that the low energy natural neutron generation rate c•（cm^-3•s^-1）varies as a rule of negative exponent of c•=2.7×10^-5e^{-0.005 7h}, when the water depth h (cm) is from 1 m to 10 m in Yi Lake. When the water depth is more than 10 m, the generation rate and fluence rate change slowly. Extrapolating from the results, the generation rate of the low energy natural neutron in water near the water surface of Yi Lake is about 2.7×10^-5cm^-3•s^-1（2.7×10^-5 g^-1•s^-1）.