Preferential flow induced by desiccation cracks (PF-DC) has been proven to be an important hydrological effect that could cause various geotechnical engineering and ecological environment problems. Investigation on the PF-DC remains a great challenge due to the soil shrinking–swelling behavior. This work presents an experimental and numerical study of the PF-DC considering the dynamic changes of desiccation cracks. A soil column test was conducted under wetting–drying cycles to investigate the dynamic changes of desiccation cracks and their hydrological response. The ratios between the crack area and soil matrix area (crack ratio), crack aperture and depth were measured. The soil water content, matrix suction and water drainage were monitored. A new dynamic dual-permeability preferential flow model (DPMDy) was developed, which includes physically consistent functions in describing the variation of both porosity and hydraulic conductivity in crack and matrix domains. Its performance was compared to the single-domain model (SDM) and rigid dual-permeability model (DPM) with fixed crack ratio and hydraulic conductivity. The experimental results showed that the maximum crack ratio and aperture decreased when the evaporation intensity was excessively raised. The self-closure phenomenon of cracks and increased surficial water content was observed during low-evaporation periods. The simulation results showed that the matrix evaporation modeled by the DPMDy is lower than that of the SDM and DPM, but its crack evaporation is the highest. Compared to the DPM, the DPMDy simulated a faster pressure head building-up process in the crack domain and higher water exchange rates from the crack to the matrix domain during rainfall. Using a fixed crack ratio in the DPM, whether it is the maximum or the average value from the experiment data, will overestimate the infiltration fluxes of PF-DC but underestimate its contribution to the matrix domain. In conclusion, the DPMDy better described the underlying physics involving crack evolution and hydrological response with respect to the SDM and DPM. Further improvement of the DPMDy should focus on the hysteresis effect of the soil water retention curve and soil deformation during wetting–drying cycles.