The conservation level of rare waterbirds reflects the quality of the regional ecological environment and wetlands, and suitable habitat patches and good environmental conditions are bases to support the activities of rare species in habitats. Establishing these conditions is also an important goal of habitat landscape and functional restoration. However, lack of these conditions limits population protection and habitat restoration of rare species. Based on the random forest (RF) algorithm and threshold indicator taxa analysis (TITAN), this paper performed habitat suitability assessment and environmental variable threshold analysis of rare waterbird species in Yancheng coastal wetlands. The results showed that the suitable area proportion of three waterbird species at different habitat sites was less than 20%. The unsuitable area proportions of red-crowned cranes and oriental storks at the CA habitat site were the highest, reaching 86.73% and 85.17%, respectively. In addition, analysis of the importance of environmental variables showed that the main influencing variables affecting the suitable habitat distribution of the three rare waterbirds were habitat type (T_hab), habitat area (A_hab), vegetation coverage (P_fvc), distance to farmland (D_far), distance to reeds (D_ree), ponds density (Ponds), distance to water surface (D_wat) and distance to main roads or seawalls (D_swa). These variables covered the type, area, coverage and distance indicators. With the exception of D_far, Ponds and D_swa, rare waterbirds had response thresholds to each environmental indicator, and these results supported the restoration of landscape structure and function of each habitat site. This study emphasized the importance of foods, water resources and hidden conditions for habitat selection in rare waterbirds. Finally, we proposed the maintenance and restoration patterns of the landscape structure and function of rare waterbird habitats, which are available for other coastal tidal wetlands. Display omitted •The spatial distributions of suitable habitats of waterbird were different.•Response thresholds of main environmental variables were calculated.•Response thresholds reflected differences in habitat requirements among waterbird species.•This study guided landscape structure and function restoration of rare waterbird habitats.