The crystallisation characteristics of freeze desalination in narrow channels need to be explored theoretically. Phase-field method (PFM) is an effective method for determining the microstructure during phase changes. In this study, the PFM coupled with the lattice Boltzmann method (LBM) was used to study the phase change behaviour and desalination effect of seawater freezing desalination in narrow channels. The phase, concentration, temperature, and flow fields were coupled and solved. A microscopy observation experimental system with a charge-coupled device camera was established to verify the numerical results. The salinity of the crystallisation zone was obtained by examining the crystallisation region. Important variables that could impact the desalination effect, such as the flow temperature, heat flux, and flow velocity, were investigated. The results showed that the flow temperature increased the desalting rate; the desalination ratio was 20 %–27.9 % in the temperature range of 263.15–283.15 K. The heat flux increased five-fold, and the desalination rate decreased from 22.6 % to 10.1 %. Owing to the counteracting effects of convection and solute diffusion on ice crystal growth, the inflow velocity had little effect on the desalination efficiency. The present method was expected to provide technical guidance for the device development of multistage crystallisers.