Two statistical models that include transit time spread and electronic noise effects are studied for evaluation of scintillation materials and for comparison of pulse shape discrimination (PSD) methods. The intrinsic PSD low-energy limitations for three scintillators are estimated by using these models, which can be used for PSD parameter optimization. Under the optimal conditions, the low-energy PSD limits of early NE213, trans-stilbene, and Borexino scintillators, are 100, 65, and 60 keV neutron energy, respectively. Calculated results show that under optimal conditions, the zero-crossing method is better for early NE213 and trans-stilbene scintillators, and the charge comparison is better for Borexino. The calculated best constant fraction discrimination (CFD) settings in the zero-crossing method for early NE213, trans-stilbene, and Borexino scintillators are 0.8, 0.8 and 0.9, respectively. The calculated best fast window settings in the charge comparison method are 0–40, 0–22, and 0–10 ns, respectively.