The Geochemical Survey of Land Quality conducted by the China Geological Survey from 1999 to 2021 collected 670321 composite surface soil samples (0-20 cm) and 167746 composite deep soil samples (150-180 cm) across approximately 2.665 million km2, covering most densely populated areas and farmland in China. Each composite sample underwent analysis for 54 chemical indicators using a standardized method (Ag, As, Au, B, Ba, Be, Bi, Br, Cd, Ce, Cl, Co, Cr, Cu, F, Ga, Ge, Hg, I, La, Li, Mn, Mo, N, Nb, Ni, P, Pb, Rb, S, Sb, Sc, Se, Sn, Sr, Th, Ti, Tl, U, V, W, Y, Zn, Zr, SiO2, Al2O3, TFe2O3, MgO, CaO, Na2O, K2O, pH, total carbon and organic carbon). This study examines the methodologies and fundamental characteristics of establishing geochemical background values, baseline values, and their upper and lower threshold limits for the 54 soil indicators in China. Additionally, it compares various thresholds of the background of cultivated soil with existing environmental and nutrient-related standards. The findings reveal that, on a national scale, most surface soil indicators exhibit content and distribution patterns inherited from deep soil, with notable changes observed only in the background values of specific indicators such as organic carbon, total carbon, N, S, Se, Hg, Br, Cd, and P. Spearman correlation coefficients for each indicator in both surface and deep soil consistently exceeded 0.50. Across the entire cultivated land in the country, only the upper limit of Cd background exceeds the risk screening value for soil contamination of agricultural land, while the upper limits of Hg, As, Pb, and Cr backgrounds were all lower than their respective risk screening values. Due to significant spatial distribution differences in many indicators, a simplistic national-scale background delineation is insufficient for refined soil resource management. Hence, the establishment of geochemical background/baseline at different scales based on national data is crucial to inform government regulations and standards for soil environmental quality management.