During the operating of nuclear reactor, the applicable condition of point reactor neutron kinetics is changed by control rods bulk insertion and reactor lattice deviating from the critical state, The measurement of reactivity, with the increase of subcriticality, shows that the results impact on the kinetic distortion effect, along with prompt neutron flux strongly deteriorated. According to the diffusion theory about prompt neutron and delayed neutron, the theoretical analysis and application of point reactor neutron kinetics have been carried out to quantify the kinetic distortion correction factors in subcritical systems, and these indicate that prompt neutron distributions are strongly affected by kinetic distortion. With the self-developed Pulsed Neutron Source measurement system, subcriticality measurement in different configuration of control rods in the zero power reactor of Nuclear Power Institute of China was carried out. In this paper the reactivity of the deep subcritical system are obtained by experiment of Pulsed Neutron Source method, meanwhile, the bias between experiment results of the areas-ratio method and the characteristic decay constant method are analyzed by comparing the condition of the experiment and the theory model, the main factors inducing the bias are found, which supplies helpful reference for other similar design and experiment.