High nature value farmland (HNVf) plays an important role in improving biodiversity and landscape heterogeneity, and it is effective in curbing soil non-point source pollution and carbon loss in sustainable eco-agricultural systems. To this end, we developed high-resolution (2 m × 2 m) indicators for the identification of potential HNVf based on GF1B remote sensing imaging, including the land cover (LC), normalized difference vegetation index (NDVI), Shannon diversity (SH), and Simpsons index (SI). The statistical results for LC with high resolution (2 m × 2 m) showed that there was 41.05% of intensive farmland in the study area, and the pixel proportion of the HNVf map (above G3) was 44.30%. These HNVf patches were concentrated in the transition zone around the edge of the intensive farmland and around rivers, with characteristics of HNVf type 2 being significantly reflected. Among the real-life areas from Map World, elements (i.e., linear forests, rivers, and semi-natural vegetation etc.) of HNVf accounted for more than 70% of these regions, while a field survey based on potential HNVf patches also exhibited significant HNVf characteristics in comparison with intensive farmlands. In addition, from 2002 to 2020, the total migration distance of the gravity center of intensive farmland in the study area was 7.65 km. Moreover, four landscape indices (patch COH index, landscape division index, SH, and SI) slowly increased, indicating that the species richness and biodiversity were improved. It was also found that a series of ecological protection policies provide effective guarantees for an improvement in species diversity and the development of HNVf in the study area. In particular, the average contents of As, Cr, Cu, Ni, and Zn in the HNVf were 20.99 mg kg−1, 121.11 mg kg−1, 21.97 mg kg−1, 29.34 mg kg−1, and 41.68 mg kg−1, respectively, which were lower in comparison with the intensive farmland soil. This is the first HNVf exploration for landscape and soil pollution assessment in a coastal delta in China, and could provide powerful guidance for the ecological protection of farmland soil and the high-quality development of sustainable agriculture.