Frost heave experiments on saturated sandstone and tuff with an open crack are conducted under uniform and unidirectional freezing conditions. Frost heave of crack in sandstone with high permeability is more significant under uniform freezing condition than that under unidirectional freezing condition. However, frost heave of crack in tuff with low permeability is more significant under unidirectional freezing condition. To illustrate the reasons for this phenomenon, a numerical model on the freezing processes of saturated rock with an open crack considering the latent heat of pore water and water in crack is proposed and confirmed to be reliable. Numerical results show that a frozen shell that blocks the migration of water in crack to rock develops first in the outer part of the rock before the freezing of water in crack under uniform freezing condition. However, the migration path of water in crack to the unfrozen rock under freezing front exists under unidirectional freezing condition. The freezing process and permeability of rock together determine the migration of water in crack and lead to the different frost heave modes of crack for various permeable rocks under different freezing conditions. The frost heave modes of crack in rock with low or high permeability are similar under uniform freezing condition because water migration is blocked by a frozen shell and is irrelevant to rock permeability. For high permeability rock, the frost heave of crack will be weakened due to water migration under unidirectional freezing condition; however, the frost heave of crack would be more significant for low permeability rock because water migration is blocked under unidirectional freezing condition. Therefore, the freezing condition and rock permeability determine the frost heave of rock with crack together, and this should be concerned in cold regions engineering applications.