More than half of all Black-faced Spoonbills, a threatened species, overwinter throughout the coastal areas of Taiwan. We used a geographic information system to develop a methodology of quantifying landscape connectivity to examine the quality and linkage of potential spoonbill habitat in Taiwan. We used number of overwintering years, maximum number of spoonbills, habitable area, and a landscape development intensity index to calculate the habitat value and connectivity of 23 selected wetlands during two different periods and to determine the least-cost path of the spoonbill for moving among habitats. During the first period (1984–2003), habitat and connectivity values were greatest in the Zengwun Estuary, confirming that it was the most suitable habitat. In the second period (2011–2014), the highest habitat value also occurred in the Zengwun Estuary, but the highest connectivity value shifted to the Sihcao wetland. The habitat and connectivity values in the second period were generally higher than those in the first period. However, in the Zengwun Estuary and Sihcao wetlands, the maximum number of spoonbills decreased as the population spread to surrounding wetlands, suggesting that habitat conditions declined in the two wetlands due to an increase in anthropogenic disturbance. The habitable wetlands with adequate connectivity were divided into three geographic groups: southwestern, northeastern, and northwestern. The habitat link of the southwestern group increased after spoonbills had been observed in several new wetlands. However, the links within the northeastern and northwestern groups decreased, as spoonbills were no longer observed in several wetlands in each group. Our results suggest that the conservation of wetlands in gap areas would improve their habitat condition and connectivity. This framework can be applied to other species and serves as a baseline for habitat linkage, corridor planning, and refuge design.