The problem of soil heavy metals (HMs) accumulation from protected cultivation (PC) needs an urgent solution. 132 soil samples from typically high-density PC areas were analyzed for accumulation, risk, and sources of 8 HMs in 16 cities of 8 provinces, China. The soil HMs accumulation characteristics were prominent; Cu, Zn, Pb, Cd, As over-standard (GB 15618-2016) rates reached 15.2, 4.5, 3.0, 27.3, and 2.3%, respectively. The single-factor pollution index indicates that Cd reached slightly contaminated levels in the whole area, while Cu was at a slightly contaminated level only in Yunnan Province. The Nemeiro comprehensive pollution index and the comprehensive quality index suggested that HMs accumulation were at the slightly contaminated levels, with Yunnan province being the most affected and Henan followed. Cu and Zn accumulations are mainly related to frequent input of organic fertilizer, especially livestock manure’s direct return to the field. Therefore, Cu and Zn showed a strong correlation (P＜0.01) with soil organic material (SOM), and their available amounts linearly correlated with the extension of planting years in PC. On the contrary, Pb and Cd amounts are only related (P＜0.01) to soil texture, and their main sources are related to the parent material of soil formation. Moreover, their available amounts did not correlate with the planting years. Our results suggest that long-term and unreasonable PC may lead to soil HMs accumulation. Therefore, appropriate agricultural materials, planting systems, and fertilization methods must be used to effectively avoid the risk of excessive HMs accumulation in the PC soils.