Land-based pollution output zoning is crucial for the integrated land-sea management and coastal sustainable development. In order to delineate the spatial extent of the land-based pollution’s generating and transporting to the corresponding nearshore marine areas in special coastal regions (such as peninsulas), which had more complex hydro-logical characteristics and longer coastline, we established a framework for the spatial zoning of land-based pollution output: Firstly we used the optimal threshold method to divide watershed zones; Secondly, we divided coastline zones based on “source-sink landscape” theory; At last, combining watershed zones on land and zones around coastline, we determined the land-based pollution output zoning on foundation of the spatial relationship of “watershed-estuaries(coastline)-bay”. Taking the Southern Liaotung Peninsula as the study area, our results revealed that: (1) Using a river network and a catchment area of 10 km² as the optimal threshold, 52 watershed zones were extracted; (2) 330 coastline zone units were divided, and the coastline zones were mainly characterized as “source” landscapes, resulting in a high risk of non-point source pollution in these areas; (3) The Southern Liaotung Peninsula could be divided into 42 land-based pollution output zones with spatial heterogeneity, and relevant measures and suggestions could be proposed based on the corresponding land use features and pollution situations of nearshore waters. Our research provides a new perspective and method for environmental governance and management in coastal regions, especially for peninsulas and islands.