Habitat loss and fragmentation have a significant negative effect on amphibian species, particularly those with specialized habitat requirements. The endangered farmland green treefrog (Zhangixalus arvalis) primarily inhabits woodlands of agricultural landscapes in central Taiwan. Recently, due to increased demands for pineapple products, many woodlands, particularly bamboo plantations, were converted to pineapple fields. This study aimed to quantify the effect of habitat loss and fragmentation on Z. arvalis due to changes in land cover in an agricultural landscape. The study area contained 34,243 50 m × 50 m grids. In 2006 and 2014-2015, we used acoustic surveys to survey the occurrence of Z. arvalis in each grid. We obtained satellite images of the study area for 2006 and 2014, and we assigned the land-cover type of each grid to one of the following six types: woodland, brushland, cropland, bareland, manmade structures and water body. We examined whether Z. arvalis preferred a certain land-cover type by comparing the proportion of cover types available and the proportion of cover types used by the frogs. Furthermore, we used occurrence records for 2006 and 2014-2015 and applied the Maximum Entropy Model to predict suitable habitat for the respective years. We mapped the loss of suitable habitat and used six indices to quantify habitat fragmentation within the 8 years. We also tested the prediction that the occupancy rate of Z. arvalis in different-sized habitat patches was a function of patch size. Zhangixalus arvalis exhibited a strong preference for woodland, but avoided cropland and manmade structures. From 2006 to 2014-2015, the suitable habitat decreased 4.1%, and all six indices showed an increase in habitat fragmentation. The occupancy rate of different-sized woodland patches was positively correlated with patch size. Mapping suitable habitat and identifying the potential gaps in functional habitat connectivity can be used to guide effective measures for conserving Z. arvalis.