Soil salinization occurs naturally in coastal areas owing to seawater intrusion and upward salt accumulation. High soil salinity limits most plants and the plant community in coastal salt marsh is mainly composed of salt-tolerant plants. The resilience of ecosystem is largely determined by the standing vegetation. However, little is known about how pioneer vegetation impacts on soil environment in coastal ecosystem, especially associated with salinization. Thus, field investigations were conducted to evaluate the difference of soil indicators in vegetation patches with that in bare lands during an intense soil salinization period in Bohai Sea coastal wasteland, North China. Root distribution for vegetation patches and soil physicochemical properties for vegetation patches and bare lands were examined in 0–20, 20–40, and 40–60 cm depth layers. The results showed that regardless of the plant species, roots in vegetation patches were mainly distributed in 0–20 cm depth and greatly promoted the soil spatial heterogeneity. Particularly, soils beneath vegetation patches exhibited higher soil total carbon content, total porosity, macro-porosity, large aggregates percentage, mean weight diameter, and saturated water content; lower bulk density, capillary porosity, soil water storage capacity, and soil electrical conductivity than that for bare lands in 0–20 cm depth. The correlation analysis among topsoil (0–20 cm) indicated that the formation of soil large aggregates and pore structure was negatively related to soil electrical conductivity. In conclusion, vegetation patches promoted the formation of soil large aggregates and macro-porosity in topsoil by root distribution. Moreover, the plant-mediated soil structure improvement enhanced the soil resistance to salt accumulation and further promoted the topsoil desalinization. The findings of this study provide some insights into the regulation of pioneer vegetation on soil environment in coastal ecosystem, supporting ecological succession and plant-mediated ecological restoration in saline lands.