Woody plant encroachment into grasslands is a worldwide phenomenon. Still, there is a research gap in quantifying the ecological processes of coastal wetland ecosystems. Here, we combined soil stable isotope technology with geostatistical methods to quantify the spatial characteristics of soil δ13C and δ15N in a coastal wetland experiencing native shrub Tamarix chinensis encroachment in the Yellow River Delta (YRD), China, and to clarify the possible mechanisms by which shrub-induced successional processes determined the spatial distribution of soil δ13C and δ15N. The results showed that soil δ13C and δ15N significantly decreased from bare land to grass and to shrub at the vegetation type level. Pearson correlation showed that soil δ13C and δ15N were positively related to soil salinity, but negatively related to plant variables (grass cover, shrub crown width and above-ground biomass). Scaling method indicated that soil δ13C variation occurred at two different scales, 40 m and 150 m, representing influences of shrub T. chinensis and environmental heterogeneity, respectively. Soil δ15N variation was observed to occur at the 75 m scale, suggesting the combination effect of T. chinensis and Suaeda glauca-dominated grass species. Furthermore, other soil and plant variables also exhibited two-scale characteristics similar to soil δ13C. Therefore, the vegetation succession processes of coastal wetlands experiencing shrub encroachment could be understood well by combining soil stable isotope with GIS spatial tools. The spatial characteristics of soil stable isotopes help us establish strategies for protecting and managing coastal wetlands.