A detection system was set up to measure the neutron generation rate of a recently developed D-D neutron generator. The system is composed of a Si detector, He-3 detector, and electronics for pulse height analysis. The neutron generation rate was measured by counting protons using the Si detector, and the data was crosschecked by counting neutrons with the He-3 detector. The efficiencies of the Si and He-3 detectors were calibrated independently by using a standard alpha particle source $^{241}Am$ and a bare isotopic neutron source $^{252}Cf$, respectively. The effect of the cross-sectional difference between the D(d,p)T and $D(d,n)^3He$ reactions was evaluated for the case of a thick target. The neutron generation rate was theoretically corrected for the anisotropic emission of protons and neutrons in the D-D reactions. The attenuations of neutron on the path to the He-3 detector by the target assembly and vacuum flange of the neutron generator were considered by the Monte Carlo method using the MCNP 4C2 code. As a result, the neutron generation rate based on the Si detector measurement was determined with a relative uncertainty of ${pm}5%$, and the two rates measured by both detectors corroborated within 20%.