One of the greatest challenges China faces is how to conserve biodiversity during intensive urban and rural development. Ecological connectivity network modelling is a planning strategy that is increasingly used to achieve habitat and biodiversity conservation goals. Often, researchers have not given enough attention to the comparison of different methods for designing and mapping ecological connectivity networks in Chinese cities. In this study, we used least-cost path and UNICOR cumulative resistant kernel analyses to simulate the ecological connectivity network across the Luohe Region of China, and used the results to prioritize ecological connectivity network linkages and core areas. Our analysis produced three main results: (1) Least-cost paths passed through all the core areas because they did not consider species’ dispersal limits. (2) Species with dispersal abilities ≤ 2 km, conversely, were predicted by resistant kernel analysis to have highly fragmented functional connectivity networks in the Luohe region, while species with dispersal abilities between 4 km and 8 km were predicted to have moderate levels of functional connectivity, and species with dispersal abilities ≥ 16 km showed high connectivity across most of the study area. (3) We identified the areas of highest functional connectivity by intersecting >75th percentile of every resistant kernel surface. This identified an area in the Yancheng district as the zone of most complete and strong connectivity. The intersection of least-cost paths with the 2 km threshold scenario of factorial least-cost paths was the first protection priority, the intersection of least-cost paths with the 8 km threshold scenario of factorial least-cost paths was the second protection priority, 8 km threshold scenario of factorial least-cost paths without core areas was the third protection priority. Our comparison of methods in mapping ecological connectivity networks is generic and can be performed in any cities with landscape configuration and species information.