Purpose Our purpose is to reveal the natural enrichment patterns of metals in the Holocene soils of the Southern Loess Plateau. Methods Element and mineral contents and particle size were measured using X-ray fluorescence spectrometry, X-ray diffractometry, and laser diffraction, respectively. Results The study area has a subtropical climate with average annual precipitation and temperature of similar to 800 mm and similar to 15.3 degrees C during the mid-Holocene. At this time the summer monsoon and non-summer monsoon supplied similar to 440 mm and similar to 360 mm of precipitation, respectively. Soil moisture was in a positive balance and persistent gravity water occurred with a moisture content > 20% in the mid-Holocene paleosol. Conclusions Natural enrichment of heavy metals occurred in the mid-Holocene paleosol, and the enrichment of heavy metals in the mid-Holocene paleosol do not meet the soil pollution standards and is safe for agricultural production. The mechanism of natural heavy metals enrichment in the mid-Holocene paleosol was as follows: The warm and humid climate enhanced the summer monsoon precipitation, causing a positive soil moisture balance, and persistent gravity water and soil moisture content > 20% caused strong leaching and hydrolysis of minerals, which resulted in enhanced clay formation and heavy metals enrichment.