Soil contamination by potentially toxic metals (PTMs) has become a public concern in China. However, the distribution and controlling factors of soil PTM fractions remain largely unknown, limiting our ability to assess their health risks and thus to make sound controlling polices. Here, we investigate the fraction distribution of cadmium (Cd) and copper (Cu) in Chinese soils and their relationships with soil pH, based on a national meta-analysis of 163 published literatures. Exchangeable Cd in southern China accounted for 19.50 ± 14.97% of total Cd, significantly (p < 0.01) higher than the corresponding 13.42 ± 6.95% in northern China. Potentially available fractions constituted about 60% of total Cd at the national scale. By contrast, about half of soil Cu existed in unavailable residual fraction. Phytoavailable (i.e., exchangeable) fraction accounted for only 2.71 ± 1.65% and 2.54 ± 1.58% of total Cu in northern and southern China, respectively. Percentages of exchangeable Cd and Cu were negatively correlated (p < 0.01) with soil pH, while potentially available fractions increased significantly (p < 0.05) with soil pH. Our results provide the first national assessment of Cd and Cu fraction distribution and their responses to soil pH variations, highlighting the necessity to consider their fraction distribution and soil properties when assessing the health risks of soil PTM contamination in China.