Quantitative investigation on the preferential flow induced by desiccation cracks (PF-DC) remains a great challenge due to the soil shrinking-swelling behavior. This work presents a series of comparative numerical studies to investigate the accuracy and substitutability of different models in simulating the water flux, hydrological response and crack evolution induced by PF-DC. As a comparative study, an effective dynamic dual-permeability model (DDPM) we recently developed and validated was regarded as a benchmark model. Three numerical experiments were conducted to (i) compare the difference among the single-domain model (SDM), rigid dual-permeability model (RDPM) and DDPM; (ii) test the sensitivity of the DDPM to the shrinking-swelling parameters; (iii) test the rationality of a “lighter” dynamic DPM (LDPM) only considering the proportion changes of each domain while neglecting the variation of hydraulic properties. The results showed that compared to the DDPM, the SDM overestimated the water content under low-rainfall intensity while underestimating the water content under high-intensity rainfall and failed to capture the early increase of water content in deep soils induced by PF-DC. The RDPM greatly overestimated the total water content and water storage capacity of the crack domain, which was not suggested to be used in the surface runoff or flood forecast. The DDPM is overall not sensitive to the shrinking-swelling parameters, indicative of relatively loose accuracy requirements in measuring the soil shrinking-swelling parameters. The LDPM can be a tentative alternative option for the DDPM, but it is better not to use it to evaluate the surface runoff or use it under long-term extreme drought. In conclusion, the prediction errors without considering crack evolution and variation of hydraulic properties of each domain (RDPM) are the highest, then followed by the only considering crack evolution (LDPM) and uncertainties of shrinking-swelling parameters.