Amphibians play a key role in structuring biological assemblages of agricultural landscapes, but they are threatened globally by agricultural intensification. Numerous studies have considered the morphology of animals to be an indicator of the health of a population, but data about the differences in amphibian morphology in different breeding habitats in agricultural landscapes are still missing. Here, we investigated the differences in the abundance and morphology of Pelophylax plancyi and Pelophylax nigromaculatus in the three waterbody types: fields, forests, and parks in agricultural landscapes in Nanjing, China. Our results emphasize that both frog species in forests and parks had significantly higher body condition indexes than those in fields, whereas their abundance in fields habitat was higher than those of the two other habitat types. Our results demonstrated the importance of non-agricultural habitats (such as forests and parks) in agricultural landscapes to the persistence of both Pelophylax species. We recommend preserving field ecosystems by constructing diverse waterbodies other than fields in rural areas and maintaining microhabitats in parks and forests to improve amphibian biodiversity in Nanjing.